Example 1 with NewCRFBean
use of org.akaza.openclinica.bean.admin.NewCRFBean in project OpenClinica by OpenClinica.
the class CreateCRFVersionServlet method processRequest.
@SuppressWarnings("unchecked")
@Override
public void processRequest() throws Exception {
resetPanel();
panel.setStudyInfoShown(true);
CRFDAO cdao = new CRFDAO(sm.getDataSource());
CRFVersionDAO vdao = new CRFVersionDAO(sm.getDataSource());
EventDefinitionCRFDAO edao = new EventDefinitionCRFDAO(sm.getDataSource());
FormProcessor fp = new FormProcessor(request);
// checks which module the requests are from
String module = fp.getString(MODULE);
// keep the module in the session
session.setAttribute(MODULE, module);
request.setAttribute("xformEnabled", CoreResources.getField("xform.enabled"));
String action = request.getParameter("action");
CRFVersionBean version = (CRFVersionBean) session.getAttribute("version");
if (StringUtil.isBlank(action)) {
logger.debug("action is blank");
request.setAttribute("version", version);
forwardPage(Page.CREATE_CRF_VERSION);
} else if ("confirm".equalsIgnoreCase(action)) {
String dir = SQLInitServlet.getField("filePath");
if (!new File(dir).exists()) {
logger.debug("The filePath in datainfo.properties is invalid " + dir);
addPageMessage(resword.getString("the_filepath_you_defined"));
forwardPage(Page.CREATE_CRF_VERSION);
// BWP 01/13/2009 >>
return;
// >>
}
// All the uploaded files will be saved in filePath/crf/original/
String theDir = dir + "crf" + File.separator + "original" + File.separator;
if (!new File(theDir).isDirectory()) {
new File(theDir).mkdirs();
logger.debug("Made the directory " + theDir);
}
// MultipartRequest multi = new MultipartRequest(request, theDir, 50 * 1024 * 1024);
String tempFile = "";
try {
tempFile = uploadFile(theDir, version);
} catch (CRFReadingException crfException) {
Validator.addError(errors, "excel_file", crfException.getMessage());
String msg = crfException.getMessage();
request.setAttribute("formMessages", errors);
forwardPage(Page.CREATE_CRF_VERSION);
return;
} catch (Exception e) {
//
logger.warn("*** Found exception during file upload***");
e.printStackTrace();
}
session.setAttribute("tempFileName", tempFile);
// provided and/or not xls format
if (errors.isEmpty()) {
String s = ((NewCRFBean) session.getAttribute("nib")).getVersionName();
if (s.length() > 255) {
Validator.addError(errors, "excel_file", resword.getString("the_version_CRF_version_more_than_255"));
} else if (s.length() <= 0) {
Validator.addError(errors, "excel_file", resword.getString("the_VERSION_column_was_blank"));
}
version.setName(s);
if (version.getCrfId() == 0) {
version.setCrfId(fp.getInt("crfId"));
}
session.setAttribute("version", version);
}
if (!errors.isEmpty()) {
logger.debug("has validation errors ");
request.setAttribute("formMessages", errors);
forwardPage(Page.CREATE_CRF_VERSION);
} else {
CRFBean crf = (CRFBean) cdao.findByPK(version.getCrfId());
ArrayList versions = (ArrayList) vdao.findAllByCRF(crf.getId());
for (int i = 0; i < versions.size(); i++) {
CRFVersionBean version1 = (CRFVersionBean) versions.get(i);
if (version.getName().equals(version1.getName())) {
// version already exists
logger.debug("Version already exists; owner or not:" + ub.getId() + "," + version1.getOwnerId());
if (ub.getId() != version1.getOwnerId()) {
// not owner
addPageMessage(respage.getString("CRF_version_try_upload_exists_database") + version1.getOwner().getName() + respage.getString("please_contact_owner_to_delete"));
forwardPage(Page.CREATE_CRF_VERSION);
return;
} else {
// owner,
ArrayList definitions = edao.findByDefaultVersion(version1.getId());
if (!definitions.isEmpty()) {
// used in
// definition
request.setAttribute("definitions", definitions);
forwardPage(Page.REMOVE_CRF_VERSION_DEF);
return;
} else {
// not used in definition
int previousVersionId = version1.getId();
version.setId(previousVersionId);
session.setAttribute("version", version);
session.setAttribute("previousVersionId", new Integer(previousVersionId));
forwardPage(Page.REMOVE_CRF_VERSION_CONFIRM);
return;
}
}
}
}
// didn't find same version in the DB,let user upload the excel
// file
logger.debug("didn't find same version in the DB,let user upload the excel file.");
// List excelErr =
// ((ArrayList)request.getAttribute("excelErrors"));
List excelErr = (ArrayList) session.getAttribute("excelErrors");
logger.debug("excelErr.isEmpty()=" + excelErr.isEmpty());
if (excelErr != null && excelErr.isEmpty()) {
addPageMessage(resword.getString("congratulations_your_spreadsheet_no_errors"));
forwardPage(Page.VIEW_SECTION_DATA_ENTRY_PREVIEW);
} else {
logger.debug("OpenClinicaException thrown, forwarding to CREATE_CRF_VERSION_CONFIRM.");
forwardPage(Page.CREATE_CRF_VERSION_CONFIRM);
}
return;
}
} else if ("confirmsql".equalsIgnoreCase(action)) {
NewCRFBean nib = (NewCRFBean) session.getAttribute("nib");
if (nib != null && nib.getItemQueries() != null) {
request.setAttribute("openQueries", nib.getItemQueries());
} else {
request.setAttribute("openQueries", new HashMap());
}
boolean canDelete = false;
// check whether need to delete previous version
Boolean deletePreviousVersion = (Boolean) session.getAttribute("deletePreviousVersion");
Integer previousVersionId = (Integer) session.getAttribute("previousVersionId");
if (deletePreviousVersion != null && deletePreviousVersion.equals(Boolean.TRUE) && previousVersionId != null && previousVersionId.intValue() > 0) {
logger.debug("Need to delete previous version");
// whether we can delete
canDelete = canDeleteVersion(previousVersionId.intValue());
if (!canDelete) {
logger.debug("but cannot delete previous version");
if (session.getAttribute("itemsHaveData") == null && session.getAttribute("eventsForVersion") == null) {
addPageMessage(respage.getString("you_are_not_owner_some_items_cannot_delete"));
}
if (session.getAttribute("itemsHaveData") == null) {
session.setAttribute("itemsHaveData", new ArrayList());
}
if (session.getAttribute("eventsForVersion") == null) {
session.setAttribute("eventsForVersion", new ArrayList());
}
forwardPage(Page.CREATE_CRF_VERSION_NODELETE);
return;
}
ArrayList<ItemBean> nonSharedItems = (ArrayList<ItemBean>) vdao.findNotSharedItemsByVersion(previousVersionId.intValue());
// htaycher: here is the trick we need to put in nib1.setItemQueries()
// update statements for shared items and insert for nonShared that were just deleted 5927
HashMap item_table_statements = new HashMap();
ArrayList<String> temp = new ArrayList<String>(nonSharedItems.size());
for (ItemBean item : nonSharedItems) {
temp.add(item.getName());
item_table_statements.put(item.getName(), nib.getBackupItemQueries().get(item.getName()));
}
for (String item_name : (Set<String>) nib.getItemQueries().keySet()) {
// check if item shared
if (!temp.contains(item_name)) {
item_table_statements.put(item_name, nib.getItemQueries().get(item_name));
}
}
// statements to run
if (!nonSharedItems.isEmpty()) {
request.setAttribute("openQueries", item_table_statements);
}
// htaycher: put all statements in
nib.setItemQueries(item_table_statements);
session.setAttribute("nib", nib);
}
// submit
logger.debug("commit sql");
NewCRFBean nib1 = (NewCRFBean) session.getAttribute("nib");
if (nib1 != null) {
try {
if (canDelete) {
nib1.deleteInsertToDB();
} else {
nib1.insertToDB();
}
request.setAttribute("queries", nib1.getQueries());
// YW << for add a link to "View CRF Version Data Entry".
// For this purpose, CRFVersion id is needed.
// So the latest CRFVersion Id of A CRF Id is it.
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
ArrayList crfvbeans = new ArrayList();
logger.debug("CRF-ID [" + version.getCrfId() + "]");
int crfVersionId = 0;
String versionOID = null;
if (version.getCrfId() != 0) {
crfvbeans = cvdao.findAllByCRFId(version.getCrfId());
CRFVersionBean cvbean = (CRFVersionBean) crfvbeans.get(crfvbeans.size() - 1);
crfVersionId = cvbean.getId();
versionOID = cvbean.getOid();
for (Iterator iter = crfvbeans.iterator(); iter.hasNext(); ) {
cvbean = (CRFVersionBean) iter.next();
if (crfVersionId < cvbean.getId()) {
crfVersionId = cvbean.getId();
}
}
}
// Not needed; crfVersionId will be autoboxed in Java 5
// this was added for the old CVS java compiler
Integer cfvID = new Integer(crfVersionId);
if (cfvID == 0) {
cfvID = cvdao.findCRFVersionId(nib1.getCrfId(), nib1.getVersionName());
}
CRFVersionBean finalVersion = (CRFVersionBean) cvdao.findByPK(cfvID);
version.setCrfId(nib1.getCrfId());
version.setOid(finalVersion.getOid());
CRFBean crfBean = (CRFBean) cdao.findByPK(version.getCrfId());
crfBean.setUpdatedDate(version.getCreatedDate());
crfBean.setUpdater(ub);
cdao.update(crfBean);
// workaround to get a correct file name below, tbh 06/2008
request.setAttribute("crfVersionId", cfvID);
// YW >>
// return those properties to initial values
session.removeAttribute("version");
session.removeAttribute("eventsForVersion");
session.removeAttribute("itemsHaveData");
session.removeAttribute("nib");
session.removeAttribute("deletePreviousVersion");
session.removeAttribute("previousVersionId");
// save new version spreadsheet
String tempFile = (String) session.getAttribute("tempFileName");
if (tempFile != null) {
logger.debug("*** ^^^ *** saving new version spreadsheet" + tempFile);
try {
String dir = SQLInitServlet.getField("filePath");
File f = new File(dir + "crf" + File.separator + "original" + File.separator + tempFile);
// check to see whether crf/new/ folder exists
// inside, if not,
// creates
// the crf/new/ folder
String finalDir = dir + "crf" + File.separator + "new" + File.separator;
if (!new File(finalDir).isDirectory()) {
logger.debug("need to create folder for excel files" + finalDir);
new File(finalDir).mkdirs();
}
// String newFile = version.getCrfId() +
// version.getName() + ".xls";
String newFile = version.getCrfId() + version.getOid() + ".xls";
logger.debug("*** ^^^ *** new file: " + newFile);
File nf = new File(finalDir + newFile);
logger.debug("copying old file " + f.getName() + " to new file " + nf.getName());
copy(f, nf);
// ?
} catch (IOException ie) {
logger.debug("==============");
addPageMessage(respage.getString("CRF_version_spreadsheet_could_not_saved_contact"));
}
}
session.removeAttribute("tempFileName");
session.removeAttribute(MODULE);
session.removeAttribute("excelErrors");
session.removeAttribute("htmlTab");
forwardPage(Page.CREATE_CRF_VERSION_DONE);
} catch (OpenClinicaException pe) {
logger.debug("--------------");
session.setAttribute("excelErrors", nib1.getErrors());
// request.setAttribute("excelErrors", nib1.getErrors());
forwardPage(Page.CREATE_CRF_VERSION_ERROR);
}
} else {
forwardPage(Page.CREATE_CRF_VERSION);
}
} else if ("delete".equalsIgnoreCase(action)) {
logger.debug("user wants to delete previous version");
List excelErr = (ArrayList) session.getAttribute("excelErrors");
logger.debug("for overwrite CRF version, excelErr.isEmpty()=" + excelErr.isEmpty());
if (excelErr != null && excelErr.isEmpty()) {
addPageMessage(resword.getString("congratulations_your_spreadsheet_no_errors"));
// should be moved to excelErr != null block
session.setAttribute("deletePreviousVersion", Boolean.TRUE);
forwardPage(Page.VIEW_SECTION_DATA_ENTRY_PREVIEW);
} else {
// should be moved to excelErr != null
session.setAttribute("deletePreviousVersion", Boolean.FALSE);
// block
logger.debug("OpenClinicaException thrown, forwarding to CREATE_CRF_VERSION_CONFIRM.");
forwardPage(Page.CREATE_CRF_VERSION_CONFIRM);
}
}
}
Also used :
ItemBean(org.akaza.openclinica.bean.submit.ItemBean)
Set(java.util.Set)
HashMap(java.util.HashMap)
ArrayList(java.util.ArrayList)
CRFReadingException(org.akaza.openclinica.exception.CRFReadingException)
OpenClinicaException(org.akaza.openclinica.exception.OpenClinicaException)
Iterator(java.util.Iterator)
ArrayList(java.util.ArrayList)
List(java.util.List)
EventDefinitionCRFDAO(org.akaza.openclinica.dao.managestudy.EventDefinitionCRFDAO)
EventCRFDAO(org.akaza.openclinica.dao.submit.EventCRFDAO)
CRFDAO(org.akaza.openclinica.dao.admin.CRFDAO)
CRFVersionDAO(org.akaza.openclinica.dao.submit.CRFVersionDAO)
FormProcessor(org.akaza.openclinica.control.form.FormProcessor)
EventDefinitionCRFDAO(org.akaza.openclinica.dao.managestudy.EventDefinitionCRFDAO)
IOException(java.io.IOException)
OpenClinicaException(org.akaza.openclinica.exception.OpenClinicaException)
InsufficientPermissionException(org.akaza.openclinica.web.InsufficientPermissionException)
CRFReadingException(org.akaza.openclinica.exception.CRFReadingException)
IOException(java.io.IOException)
NewCRFBean(org.akaza.openclinica.bean.admin.NewCRFBean)
CRFBean(org.akaza.openclinica.bean.admin.CRFBean)
NewCRFBean(org.akaza.openclinica.bean.admin.NewCRFBean)
CRFVersionBean(org.akaza.openclinica.bean.submit.CRFVersionBean)
File(java.io.File)
Example 2 with NewCRFBean
use of org.akaza.openclinica.bean.admin.NewCRFBean in project OpenClinica by OpenClinica.
the class DeleteCRFVersionServlet method processRequest.
@Override
public void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
int versionId = fp.getInt(VERSION_ID, true);
String action = request.getParameter("action");
if (versionId == 0) {
addPageMessage(respage.getString("please_choose_a_CRF_version_to_delete"));
forwardPage(Page.CRF_LIST_SERVLET);
} else {
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
CRFDAO cdao = new CRFDAO(sm.getDataSource());
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
StudyEventDefinitionDAO sedDao = new StudyEventDefinitionDAO(sm.getDataSource());
StudyEventDAO seDao = new StudyEventDAO(sm.getDataSource());
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
CRFVersionBean version = (CRFVersionBean) cvdao.findByPK(versionId);
// find definitions using this version
ArrayList definitions = edcdao.findByDefaultVersion(version.getId());
for (Object edcBean : definitions) {
StudyEventDefinitionBean sedBean = (StudyEventDefinitionBean) sedDao.findByPK(((EventDefinitionCRFBean) edcBean).getStudyEventDefinitionId());
((EventDefinitionCRFBean) edcBean).setEventName(sedBean.getName());
}
// find event crfs using this version
ArrayList<ItemDataBean> idBeans = iddao.findByCRFVersion(version);
ArrayList<EventCRFBean> eCRFs = ecdao.findAllByCRF(version.getCrfId());
for (EventCRFBean eCRF : eCRFs) {
StudySubjectBean ssBean = (StudySubjectBean) ssdao.findByPK(eCRF.getStudySubjectId());
eCRF.setStudySubject(ssBean);
StudyEventBean seBean = (StudyEventBean) seDao.findByPK(eCRF.getStudyEventId());
StudyEventDefinitionBean sedBean = (StudyEventDefinitionBean) sedDao.findByPK(seBean.getStudyEventDefinitionId());
seBean.setStudyEventDefinition(sedBean);
eCRF.setStudyEvent(seBean);
}
ArrayList eventCRFs = ecdao.findAllByCRFVersion(versionId);
boolean canDelete = true;
if (!definitions.isEmpty()) {
// used in definition
canDelete = false;
request.setAttribute("definitions", definitions);
addPageMessage(respage.getString("this_CRF_version") + " " + version.getName() + respage.getString("has_associated_study_events_definitions_cannot_delete"));
} else if (!idBeans.isEmpty()) {
canDelete = false;
request.setAttribute("eventCRFs", eCRFs);
request.setAttribute("itemDataForVersion", idBeans);
addPageMessage(respage.getString("this_CRF_version") + " " + version.getName() + respage.getString("has_associated_item_data_cannot_delete"));
} else if (!eventCRFs.isEmpty()) {
canDelete = false;
request.setAttribute("eventsForVersion", eventCRFs);
addPageMessage(respage.getString("this_CRF_version") + " " + version.getName() + respage.getString("has_associated_study_events_cannot_delete"));
}
if ("confirm".equalsIgnoreCase(action)) {
request.setAttribute(VERSION_TO_DELETE, version);
forwardPage(Page.DELETE_CRF_VERSION);
} else {
// submit
if (canDelete) {
ArrayList items = cvdao.findNotSharedItemsByVersion(versionId);
NewCRFBean nib = new NewCRFBean(sm.getDataSource(), version.getCrfId());
nib.setDeleteQueries(cvdao.generateDeleteQueries(versionId, items));
nib.deleteFromDB();
addPageMessage(respage.getString("the_CRF_version_has_been_deleted_succesfully"));
} else {
addPageMessage(respage.getString("the_CRF_version_cannot_be_deleted"));
}
forwardPage(Page.CRF_LIST_SERVLET);
}
}
}
Also used :
EventDefinitionCRFDAO(org.akaza.openclinica.dao.managestudy.EventDefinitionCRFDAO)
EventCRFDAO(org.akaza.openclinica.dao.submit.EventCRFDAO)
CRFDAO(org.akaza.openclinica.dao.admin.CRFDAO)
CRFVersionDAO(org.akaza.openclinica.dao.submit.CRFVersionDAO)
FormProcessor(org.akaza.openclinica.control.form.FormProcessor)
ArrayList(java.util.ArrayList)
StudyEventDefinitionBean(org.akaza.openclinica.bean.managestudy.StudyEventDefinitionBean)
EventDefinitionCRFDAO(org.akaza.openclinica.dao.managestudy.EventDefinitionCRFDAO)
StudyEventBean(org.akaza.openclinica.bean.managestudy.StudyEventBean)
StudySubjectDAO(org.akaza.openclinica.dao.managestudy.StudySubjectDAO)
ItemDataDAO(org.akaza.openclinica.dao.submit.ItemDataDAO)
EventCRFBean(org.akaza.openclinica.bean.submit.EventCRFBean)
NewCRFBean(org.akaza.openclinica.bean.admin.NewCRFBean)
StudyEventDefinitionDAO(org.akaza.openclinica.dao.managestudy.StudyEventDefinitionDAO)
StudySubjectBean(org.akaza.openclinica.bean.managestudy.StudySubjectBean)
ItemDataBean(org.akaza.openclinica.bean.submit.ItemDataBean)
StudyEventDAO(org.akaza.openclinica.dao.managestudy.StudyEventDAO)
CRFVersionBean(org.akaza.openclinica.bean.submit.CRFVersionBean)
EventDefinitionCRFBean(org.akaza.openclinica.bean.managestudy.EventDefinitionCRFBean)
EventCRFDAO(org.akaza.openclinica.dao.submit.EventCRFDAO)
Example 3 with NewCRFBean
use of org.akaza.openclinica.bean.admin.NewCRFBean in project OpenClinica by OpenClinica.
the class CreateCRFVersionServlet method canDeleteVersion.
/**
* Checks whether the version can be deleted
*
* @param previousVersionId
* @return
*/
private boolean canDeleteVersion(int previousVersionId) {
CRFVersionDAO cdao = new CRFVersionDAO(sm.getDataSource());
ArrayList items = null;
ArrayList itemsHaveData = new ArrayList();
// boolean isItemUsedByOtherVersion =
// cdao.isItemUsedByOtherVersion(previousVersionId);
// if (isItemUsedByOtherVersion) {
// ArrayList itemsUsedByOtherVersion = (ArrayList)
// cdao.findItemUsedByOtherVersion(previousVersionId);
// session.setAttribute("itemsUsedByOtherVersion",itemsUsedByOtherVersion);
// return false;
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
ArrayList events = ecdao.findAllByCRFVersion(previousVersionId);
if (!events.isEmpty()) {
session.setAttribute("eventsForVersion", events);
return false;
}
items = cdao.findNotSharedItemsByVersion(previousVersionId);
for (int i = 0; i < items.size(); i++) {
ItemBean item = (ItemBean) items.get(i);
if (ub.getId() != item.getOwner().getId()) {
logger.debug("not owner" + item.getOwner().getId() + "<>" + ub.getId());
return false;
}
if (cdao.hasItemData(item.getId())) {
itemsHaveData.add(item);
logger.debug("item has data");
session.setAttribute("itemsHaveData", itemsHaveData);
return false;
}
}
// user is the owner and item not have data,
// delete previous version with non-shared items
NewCRFBean nib = (NewCRFBean) session.getAttribute("nib");
nib.setDeleteQueries(cdao.generateDeleteQueries(previousVersionId, items));
session.setAttribute("nib", nib);
return true;
}
Also used :
ItemBean(org.akaza.openclinica.bean.submit.ItemBean)
NewCRFBean(org.akaza.openclinica.bean.admin.NewCRFBean)
CRFVersionDAO(org.akaza.openclinica.dao.submit.CRFVersionDAO)
ArrayList(java.util.ArrayList)
EventCRFDAO(org.akaza.openclinica.dao.submit.EventCRFDAO)
Example 4 with NewCRFBean
use of org.akaza.openclinica.bean.admin.NewCRFBean in project OpenClinica by OpenClinica.
the class CreateCRFVersionServlet method uploadFile.
/**
* Uploads the excel version file
*
* @param version
* @throws Exception
*/
public String uploadFile(String theDir, CRFVersionBean version) throws Exception {
List<File> theFiles = uploadHelper.returnFiles(request, context, theDir);
// Enumeration files = multi.getFileNames();
errors.remove("excel_file");
String tempFile = null;
for (File f : theFiles) {
// File f = multi.getFile(name);
if (f == null || f.getName() == null) {
logger.debug("file is empty.");
Validator.addError(errors, "excel_file", resword.getString("you_have_to_provide_spreadsheet"));
session.setAttribute("version", version);
return tempFile;
} else if (f.getName().indexOf(".xls") < 0 && f.getName().indexOf(".XLS") < 0) {
logger.debug("file name:" + f.getName());
Validator.addError(errors, "excel_file", respage.getString("file_you_uploaded_not_seem_excel_spreadsheet"));
session.setAttribute("version", version);
return tempFile;
} else {
logger.debug("file name:" + f.getName());
tempFile = f.getName();
// create the inputstream here, so that it can be enclosed in a
// try/finally block and closed :: BWP, 06/08/2007
FileInputStream inStream = null;
FileInputStream inStreamClassic = null;
SpreadSheetTableRepeating htab = null;
SpreadSheetTableClassic sstc = null;
// create newCRFBean here
NewCRFBean nib = null;
try {
inStream = new FileInputStream(theDir + tempFile);
// *** now change the code here to generate sstable, tbh
// 06/07
htab = new SpreadSheetTableRepeating(inStream, ub, // FileInputStream(theDir + tempFile), ub,
version.getName(), locale, currentStudy.getId());
htab.setMeasurementUnitDao((MeasurementUnitDao) SpringServletAccess.getApplicationContext(context).getBean("measurementUnitDao"));
if (!htab.isRepeating()) {
inStreamClassic = new FileInputStream(theDir + tempFile);
sstc = new SpreadSheetTableClassic(inStreamClassic, ub, version.getName(), locale, currentStudy.getId());
sstc.setMeasurementUnitDao((MeasurementUnitDao) SpringServletAccess.getApplicationContext(context).getBean("measurementUnitDao"));
}
if (htab.isRepeating()) {
htab.setCrfId(version.getCrfId());
// not the best place for this but for now...
session.setAttribute("new_table", "y");
} else {
sstc.setCrfId(version.getCrfId());
}
if (htab.isRepeating()) {
nib = htab.toNewCRF(sm.getDataSource(), respage);
} else {
nib = sstc.toNewCRF(sm.getDataSource(), respage);
}
// bwp; 2/28/07; updated 6/11/07;
// This object is created to pull preview information out of
// the
// spreadsheet
HSSFWorkbook workbook = null;
FileInputStream inputStream = null;
try {
inputStream = new FileInputStream(theDir + tempFile);
workbook = new HSSFWorkbook(inputStream);
// Store the Sections, Items, Groups, and CRF name and
// version information
// so they can be displayed in a preview. The Map
// consists of the
// names "sections," "items," "groups," and "crf_info"
// as keys, each of which point
// to a Map containing data on those CRF sections.
// Check if it's the old template
Preview preview;
if (htab.isRepeating()) {
// the preview uses date formatting with default
// values in date fields: yyyy-MM-dd
preview = new SpreadsheetPreviewNw();
} else {
preview = new SpreadsheetPreview();
}
session.setAttribute("preview_crf", preview.createCrfMetaObject(workbook));
} catch (Exception exc) {
// opening the stream could
// throw FileNotFoundException
exc.printStackTrace();
String message = resword.getString("the_application_encountered_a_problem_uploading_CRF");
logger.debug(message + ": " + exc.getMessage());
this.addPageMessage(message);
} finally {
if (inputStream != null) {
try {
inputStream.close();
} catch (IOException io) {
// ignore this close()-related exception
}
}
}
ArrayList ibs = isItemSame(nib.getItems(), version);
if (!ibs.isEmpty()) {
ArrayList warnings = new ArrayList();
warnings.add(resexception.getString("you_may_not_modify_items"));
for (int i = 0; i < ibs.size(); i++) {
ItemBean ib = (ItemBean) ibs.get(i);
if (ib.getOwner().getId() == ub.getId()) {
warnings.add(resword.getString("the_item") + " '" + ib.getName() + "' " + resexception.getString("in_your_spreadsheet_already_exists") + ib.getDescription() + "), DATA_TYPE(" + ib.getDataType().getName() + "), UNITS(" + ib.getUnits() + "), " + resword.getString("and_or") + " PHI_STATUS(" + ib.isPhiStatus() + "). UNITS " + resword.getString("and") + " DATA_TYPE(PDATE to DATE) " + resexception.getString("will_not_be_changed_if") + " PHI, DESCRIPTION, DATA_TYPE from PDATE to DATE " + resexception.getString("will_be_changed_if_you_continue"));
} else {
warnings.add(resword.getString("the_item") + " '" + ib.getName() + "' " + resexception.getString("in_your_spreadsheet_already_exists") + ib.getDescription() + "), DATA_TYPE(" + ib.getDataType().getName() + "), UNITS(" + ib.getUnits() + "), " + resword.getString("and_or") + " PHI_STATUS(" + ib.isPhiStatus() + "). " + resexception.getString("these_field_cannot_be_modified_because_not_owner"));
}
request.setAttribute("warnings", warnings);
}
}
ItemBean ib = isResponseValid(nib.getItems(), version);
if (ib != null) {
nib.getErrors().add(resword.getString("the_item") + ": " + ib.getName() + " " + resexception.getString("in_your_spreadsheet_already_exits_in_DB"));
}
} catch (IOException io) {
logger.warn("Opening up the Excel file caused an error. the error message is: " + io.getMessage());
} finally {
if (inStream != null) {
try {
inStream.close();
} catch (IOException ioe) {
}
}
if (inStreamClassic != null) {
try {
inStreamClassic.close();
} catch (IOException ioe) {
}
}
}
// request.setAttribute("excelErrors", .getErrors());
session.setAttribute("excelErrors", nib.getErrors());
session.setAttribute("htmlTable", nib.getHtmlTable());
session.setAttribute("nib", nib);
}
}
return tempFile;
}
Also used :
ItemBean(org.akaza.openclinica.bean.submit.ItemBean)
MeasurementUnitDao(org.akaza.openclinica.dao.hibernate.MeasurementUnitDao)
ArrayList(java.util.ArrayList)
IOException(java.io.IOException)
FileInputStream(java.io.FileInputStream)
HSSFWorkbook(org.apache.poi.hssf.usermodel.HSSFWorkbook)
OpenClinicaException(org.akaza.openclinica.exception.OpenClinicaException)
InsufficientPermissionException(org.akaza.openclinica.web.InsufficientPermissionException)
CRFReadingException(org.akaza.openclinica.exception.CRFReadingException)
IOException(java.io.IOException)
NewCRFBean(org.akaza.openclinica.bean.admin.NewCRFBean)
File(java.io.File)
Example 5 with NewCRFBean
use of org.akaza.openclinica.bean.admin.NewCRFBean in project OpenClinica by OpenClinica.
the class SpreadSheetTableClassic method toNewCRF.
public NewCRFBean toNewCRF(javax.sql.DataSource ds, ResourceBundle resPageMsg) throws IOException, CRFReadingException {
String dbName = SQLInitServlet.getDBName();
NewCRFBean ncrf = new NewCRFBean(ds, crfId);
// set crf id
ncrf.setCrfId(crfId);
StringBuffer buf = new StringBuffer();
HSSFWorkbook wb = new HSSFWorkbook(fs);
int numSheets = wb.getNumberOfSheets();
ArrayList queries = new ArrayList();
ArrayList errors = new ArrayList();
ArrayList repeats = new ArrayList();
HashMap tableNames = new HashMap();
HashMap items = new HashMap();
String pVersion = "";
String pVerDesc = "";
int parentId = 0;
// default is ST(String) type
int dataTypeId = 5;
HashMap itemCheck = ncrf.getItemNames();
HashMap GroupCheck = ncrf.getItemGroupNames();
HashMap openQueries = new LinkedHashMap();
// save all the item
HashMap backupItemQueries = new LinkedHashMap();
// queries if
// deleting item happens
// check for dupes, also
ArrayList secNames = new ArrayList();
// YW 1-30-2008
HashMap<String, String> allItems = new HashMap<String, String>();
ArrayList<String> itemGroupOids = new ArrayList<String>();
ArrayList<String> itemOids = new ArrayList<String>();
CRFDAO cdao = new CRFDAO(ds);
CRFBean crf = (CRFBean) cdao.findByPK(crfId);
ItemDataDAO iddao = new ItemDataDAO(ds);
ItemDAO idao = new ItemDAO(ds);
CRFVersionDAO cvdao = new CRFVersionDAO(ds);
ItemGroupDAO itemGroupDao = new ItemGroupDAO(ds);
int validSheetNum = 0;
for (int j = 0; j < numSheets; j++) {
// sheetIndex);
HSSFSheet sheet = wb.getSheetAt(j);
String sheetName = wb.getSheetName(j);
if (sheetName.equalsIgnoreCase("CRF") || sheetName.equalsIgnoreCase("Sections") || sheetName.equalsIgnoreCase("Items")) {
validSheetNum++;
}
}
if (validSheetNum != 3) {
// errors.add("The excel spreadsheet doesn't have required valid
// worksheets. Please check whether it contains" +
// " sheets of CRF, Sections and Items.");
errors.add(resPageMsg.getString("excel_not_have_valid_worksheet"));
}
// 7/30
for (int j = 0; j < numSheets; j++) {
// sheetIndex);
HSSFSheet sheet = wb.getSheetAt(j);
String sheetName = wb.getSheetName(j);
if (sheetName.equalsIgnoreCase("Instructions")) {
// totally ignore instructions
} else {
/*
* current strategem: build out the queries by hand and revisit
* this as part of the data loading module. We begin to check
* for errors here and look for blank cells where there should
* be data, tbh, 7/28
*/
int numRows = sheet.getPhysicalNumberOfRows();
int lastNumRow = sheet.getLastRowNum();
// logger.info("PhysicalNumberOfRows" +
// sheet.getPhysicalNumberOfRows());
logger.info("PhysicalNumberOfRows" + sheet.getPhysicalNumberOfRows());
// logger.info("LastRowNum()" + sheet.getLastRowNum());
String secName = "";
String page = "";
// records all the
ArrayList resNames = new ArrayList();
// response_labels
HashMap htmlErrors = new HashMap();
// the above two need to persist across mult. queries,
// and they should be created FIRST anyway, since instrument is
// first
// also need to add to VERSIONING_MAP, tbh, 6-6-3
// try to count how many blank rows, if 5 concective blank rows
// found, stop reading
int blankRowCount = 0;
if (sheetName.equalsIgnoreCase("Items")) {
logger.info("read an item in sheet" + sheetName);
Map labelWithType = new HashMap<String, String>();
// let's insert the default group first
ItemGroupBean defaultGroup = new ItemGroupBean();
defaultGroup.setName("Ungrouped");
defaultGroup.setCrfId(crfId);
defaultGroup.setStatus(Status.AVAILABLE);
// Create oid for Item Group
String defaultGroupOid = itemGroupDao.getValidOid(defaultGroup, crfName, defaultGroup.getName(), itemGroupOids);
itemGroupOids.add(defaultGroupOid);
String defaultSql = "";
if (dbName.equals("oracle")) {
/*defaultSql =
"INSERT INTO ITEM_GROUP ( " + "name, crf_id, status_id, date_created ,owner_id,oc_oid)" + "VALUES ('" + defaultGroup.getName()
+ "', " + defaultGroup.getCrfId() + "," + defaultGroup.getStatus().getId() + "," + "sysdate," + ub.getId() + ",'"
+ defaultGroupOid + "')";*/
defaultSql = "INSERT INTO ITEM_GROUP ( name, crf_id, status_id, date_created ,owner_id,oc_oid)" + " VALUES (?, ?, ?,sysdate, ?, ?)";
} else {
/* defaultSql =
"INSERT INTO ITEM_GROUP ( " + "name, crf_id, status_id, date_created ,owner_id,oc_oid)" + "VALUES ('" + defaultGroup.getName()
+ "', " + defaultGroup.getCrfId() + "," + defaultGroup.getStatus().getId() + "," + "now()," + ub.getId() + ",'"
+ defaultGroupOid + "')";*/
defaultSql = "INSERT INTO ITEM_GROUP ( name, crf_id, status_id, date_created ,owner_id,oc_oid)" + " VALUES (?, ?, ?,now(), ?, ?)";
}
if (!GroupCheck.containsKey("Ungrouped")) {
ArrayList<SqlParameter> sqlParameters = new ArrayList<>();
sqlParameters.add(new SqlParameter(defaultGroup.getName()));
sqlParameters.add(new SqlParameter(defaultGroup.getCrfId().toString(), JDBCType.INTEGER));
sqlParameters.add(new SqlParameter(defaultGroup.getStatus().getId() + "", JDBCType.INTEGER));
sqlParameters.add(new SqlParameter(ub.getId() + "", JDBCType.INTEGER));
sqlParameters.add(new SqlParameter(defaultGroupOid + "", JDBCType.INTEGER));
QueryObject qo = new QueryObject();
qo.setSql(defaultSql);
qo.setSqlParameters(sqlParameters);
queries.add(qo);
}
// Adding itemnames for further use
HashMap itemNames = new HashMap();
for (int k = 1; k < numRows; k++) {
HSSFCell cell = sheet.getRow(k).getCell((short) 0);
String itemName = getValue(cell);
itemName = itemName.replaceAll("<[^>]*>", "");
itemNames.put(k, itemName);
}
for (int k = 1; k < numRows; k++) {
// logger.info("hit row "+k);
if (blankRowCount == 5) {
logger.info("hit end of the row ");
break;
}
if (sheet.getRow(k) == null) {
blankRowCount++;
continue;
}
HSSFCell cell = sheet.getRow(k).getCell((short) 0);
String itemName = getValue(cell);
itemName = itemName.replaceAll("<[^>]*>", "");
// regexp to make sure it is all word characters, '\w+' in regexp terms
if (!Utils.isMatchingRegexp(itemName, "\\w+")) {
// different item error to go here
errors.add(resPageMsg.getString("item_name_column") + " " + resPageMsg.getString("was_invalid_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ". " + resPageMsg.getString("you_can_only_use_letters_or_numbers"));
htmlErrors.put(j + "," + k + ",0", resPageMsg.getString("INVALID_FIELD"));
}
if (StringUtil.isBlank(itemName)) {
// errors.add("The ITEM_NAME column was blank at row
// " + k + ", Items worksheet.");
// htmlErrors.put(j + "," + k + ",0", "REQUIRED
// FIELD");
errors.add(resPageMsg.getString("item_name_column") + " " + resPageMsg.getString("was_blank_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ". ");
htmlErrors.put(j + "," + k + ",0", resPageMsg.getString("required_field"));
}
if (itemName != null && itemName.length() > 255) {
errors.add(resPageMsg.getString("item_name_length_error"));
}
if (repeats.contains(itemName)) {
// errors.add("A duplicate ITEM_NAME of " + itemName
// + " was detected at row " + k
// + ", Items worksheet.");
// htmlErrors.put(j + "," + k + ",0", "DUPLICATE
// FIELD");
errors.add(resPageMsg.getString("duplicate") + " " + resPageMsg.getString("item_name_column") + " " + itemName + " " + resPageMsg.getString("was_detected_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + "," + k + ",0", resPageMsg.getString("required_field"));
} else if (itemName.length() > 0) {
allItems.put(itemName, "Ungrouped");
}
repeats.add(itemName);
cell = sheet.getRow(k).getCell((short) 1);
String descLabel = getValue(cell);
descLabel = descLabel.replaceAll("<[^>]*>", "");
if (StringUtil.isBlank(descLabel)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("DESCRIPTION_LABEL_column") + " " + resPageMsg.getString("was_blank_at_row") + " " + k + "," + resPageMsg.getString("items_worksheet") + ".");
// errors.add("The DESCRIPTION_LABEL column was
// blank at row " + k + "," +
// resPageMsg.getString("items_worksheet") +".");
htmlErrors.put(j + "," + k + ",1", resPageMsg.getString("required_field"));
}
if (descLabel != null && descLabel.length() > 4000) {
errors.add(resPageMsg.getString("item_desc_length_error"));
}
cell = sheet.getRow(k).getCell((short) 2);
String leftItemText = getValue(cell);
if (leftItemText != null && leftItemText.length() > 4000) {
errors.add(resPageMsg.getString("left_item_length_error"));
}
// Commented out to resolve issue-2413
// if (StringUtil.isBlank(leftItemText)) {
// errors.add(resPageMsg.getString("the") + " " +
// resPageMsg.getString("LEFT_ITEM_TEXT_column") + " "
// + resPageMsg.getString("was_blank_at_row") + k + ","
// + resPageMsg.getString("items_worksheet") + ".");
// htmlErrors.put(j + "," + k + ",2",
// resPageMsg.getString("required_field"));
// }
cell = sheet.getRow(k).getCell((short) 3);
String unit = getValue(cell).trim();
if (unit != null && unit.length() > 0) {
String muSql = "";
if (this.existingUnits.size() > 0) {
} else {
this.existingUnits = this.measurementUnitDao.findAllNamesInUpperCase();
if (this.existingUnits == null) {
this.existingUnits = new TreeSet<String>();
}
}
if (this.existingOIDs.size() > 0) {
} else {
this.existingOIDs = this.measurementUnitDao.findAllOIDs();
if (this.existingOIDs == null) {
this.existingOIDs = new TreeSet<String>();
}
}
if (this.existingUnits.contains(unit.toUpperCase())) {
this.logger.error("unit=" + unit + " existed.");
} else {
String oid = "";
try {
oid = new MeasurementUnitOidGenerator().generateOidNoValidation(unit);
} catch (Exception e) {
throw new RuntimeException("CANNOT GENERATE OID");
}
if (this.existingOIDs.contains(oid)) {
if (oid.length() > 40) {
oid = oid.substring(0, 35);
}
oid = new MeasurementUnitOidGenerator().randomizeOid(oid);
}
this.existingOIDs.add(oid);
this.existingUnits.add(unit.toUpperCase());
muSql = this.getMUInsertSqlParameters();
ArrayList<SqlParameter> sqlParameters = new ArrayList<>();
sqlParameters.add(new SqlParameter(oid));
sqlParameters.add(new SqlParameter(unit));
QueryObject qo = new QueryObject();
qo.setSql(muSql);
qo.setSqlParameters(sqlParameters);
queries.add(qo);
}
}
cell = sheet.getRow(k).getCell((short) 4);
String rightItemText = getValue(cell);
if (rightItemText != null && rightItemText.length() > 2000) {
errors.add(resPageMsg.getString("right_item_length_error"));
}
cell = sheet.getRow(k).getCell((short) 5);
if (cell != null) {
secName = getValue(cell);
secName = secName.replaceAll("<[^>]*>", "");
}
if (secName != null && secName.length() > 2000) {
errors.add(resPageMsg.getString("section_label_length_error"));
}
if (!secNames.contains(secName)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("SECTION_LABEL_column") + " " + resPageMsg.getString("not_valid_section_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ". " + resPageMsg.getString("check_to_see_that_there_is_valid_LABEL"));
htmlErrors.put(j + "," + k + ",5", resPageMsg.getString("NOT_A_VALID_LABEL"));
}
cell = sheet.getRow(k).getCell((short) 6);
String header = getValue(cell);
if (header != null && header.length() > 2000) {
errors.add(resPageMsg.getString("item_header_length_error"));
}
cell = sheet.getRow(k).getCell((short) 7);
String subHeader = getValue(cell);
if (subHeader != null && subHeader.length() > 240) {
errors.add(resPageMsg.getString("item_subheader_length_error"));
}
cell = sheet.getRow(k).getCell((short) 8);
String parentItem = getValue(cell);
parentItem = parentItem.replaceAll("<[^>]*>", "");
// Checking for a valid paren item name
if (!StringUtil.isBlank(parentItem)) {
if (!itemNames.containsValue(parentItem)) {
errors.add("the Parent item specified on row " + k + " does not exist in the CRF template. Please update the value. ");
}
}
// BWP>>Prevent parent names that equal the Item names
if (itemName != null && itemName.equalsIgnoreCase(parentItem)) {
parentItem = "";
}
cell = sheet.getRow(k).getCell((short) 9);
int columnNum = 0;
String column = getValue(cell);
if (!StringUtil.isBlank(column)) {
try {
columnNum = Integer.parseInt(column);
} catch (NumberFormatException ne) {
columnNum = 0;
}
}
cell = sheet.getRow(k).getCell((short) 10);
if (cell != null) {
page = getValue(cell);
}
cell = sheet.getRow(k).getCell((short) 11);
String questionNum = getValue(cell);
cell = sheet.getRow(k).getCell((short) 12);
String responseType = getValue(cell);
int responseTypeId = 1;
if (StringUtil.isBlank(responseType)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("RESPONSE_TYPE_column") + " " + resPageMsg.getString("was_blank_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + "," + k + ",12", resPageMsg.getString("required_field"));
} else {
if (!ResponseType.findByName(responseType.toLowerCase())) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("RESPONSE_TYPE_column") + " " + resPageMsg.getString("was_invalid_at_row") + k + ", " + resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + "," + k + ",12", resPageMsg.getString("INVALID_FIELD"));
} else {
responseTypeId = ResponseType.getByName(responseType.toLowerCase()).getId();
}
}
cell = sheet.getRow(k).getCell((short) 13);
String responseLabel = getValue(cell);
// "");
if (StringUtil.isBlank(responseLabel) && responseTypeId != ResponseType.TEXT.getId() && responseTypeId != ResponseType.TEXTAREA.getId()) {
// << tbh #4180
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("RESPONSE_LABEL_column") + " " + resPageMsg.getString("was_blank_at_row") + k + ", " + resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + "," + k + ",13", resPageMsg.getString("required_field"));
} else if ("file".equalsIgnoreCase(responseType) && !"file".equalsIgnoreCase(responseLabel)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("RESPONSE_LABEL_column") + " " + resPageMsg.getString("should_be_file") + resPageMsg.getString("at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + "," + k + ",13", resPageMsg.getString("should_be_file"));
}
cell = sheet.getRow(k).getCell((short) 14);
String resOptions = getValue(cell);
// resOptions = resOptions.replaceAll("<[^>]*>", "");
if (responseLabel.equalsIgnoreCase("text") || responseLabel.equalsIgnoreCase("textarea")) {
resOptions = "text";
}
if ("file".equalsIgnoreCase(responseType)) {
resOptions = "file";
}
// YW 2-5-2008 << set default resOptions for calculation
// and group-calculation type
// if(responseTypeId==8 || responseTypeId==9) {
// resOptions = resOptions.length()>0 ? resOptions :
// "can not calculate";
// }
// YW >>
int numberOfOptions = 0;
if (!resNames.contains(responseLabel) && StringUtil.isBlank(resOptions) && responseTypeId != ResponseType.TEXT.getId() && responseTypeId != ResponseType.TEXTAREA.getId()) {
// << tbh #4180
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("RESPONSE_OPTIONS_TEXT_column") + resPageMsg.getString("was_blank_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + "," + k + ",14", resPageMsg.getString("required_field"));
}
if (!resNames.contains(responseLabel) && !StringUtil.isBlank(resOptions)) {
// old template
if (responseTypeId == 8 || responseTypeId == 9) {
numberOfOptions = 1;
// YW >>
} else {
// String[] resArray = resOptions.split(",");
String text1 = resOptions.replaceAll("\\\\,", "##");
String[] resArray = text1.split(",");
numberOfOptions = resArray.length;
}
}
cell = sheet.getRow(k).getCell((short) 15);
String resValues = getValue(cell);
String value1 = resValues.replaceAll("\\\\,", "##");
String[] resValArray = value1.split(",");
if (responseLabel.equalsIgnoreCase("text") || responseLabel.equalsIgnoreCase("textarea")) {
resValues = "text";
}
if ("file".equalsIgnoreCase(responseType)) {
resValues = "file";
}
if (!resNames.contains(responseLabel) && StringUtil.isBlank(resValues) && responseTypeId != ResponseType.TEXT.getId() && responseTypeId != ResponseType.TEXTAREA.getId()) {
// << tbh, #4180, add textarea too?
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("RESPONSE_VALUES_column") + " " + resPageMsg.getString("was_blank_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + "," + k + ",15", resPageMsg.getString("required_field"));
}
// YW 1-25-2008 << validate scoring expression
if (responseTypeId == 8 || responseTypeId == 9) {
// func, it must be correctly spelled
if (resValues.contains(":")) {
String[] s = resValues.split(":");
if (!"func".equalsIgnoreCase(s[0].trim())) {
errors.add(resPageMsg.getString("expression_not_start_with_func_at") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ". ");
htmlErrors.put(j + "," + k + ",15", resPageMsg.getString("INVALID_FIELD"));
}
}
String exp = resValues;
// make both \\, and , works for functions
exp = exp.replace("\\\\,", "##");
exp = exp.replace("##", ",");
exp = exp.replace(",", "\\\\,");
resValues = exp;
if (exp.startsWith("func:")) {
exp = exp.substring(5).trim();
}
exp = exp.replace("\\\\,", "##");
StringBuffer err = new StringBuffer();
ArrayList<String> variables = new ArrayList<String>();
ScoreValidator scoreValidator = new ScoreValidator(locale);
if (!scoreValidator.isValidExpression(exp, err, variables)) {
errors.add(resPageMsg.getString("expression_invalid_at") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ": " + err);
htmlErrors.put(j + "," + k + ",15", resPageMsg.getString("INVALID_FIELD"));
}
String group = "Ungrouped";
for (String v : variables) {
if (!allItems.containsKey(v)) {
errors.add(resPageMsg.getString("item") + v + resPageMsg.getString("must_listed_before_item") + itemName + resPageMsg.getString("item_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ". ");
htmlErrors.put(j + "," + k + ",15", resPageMsg.getString("INVALID_FIELD"));
}
}
} else if (numberOfOptions > 0) {
// YW >>
if (resValArray.length != numberOfOptions) {
errors.add(resPageMsg.getString("incomplete_option_value_pair") + " " + resPageMsg.getString("RESPONSE_OPTIONS_column") + " " + resPageMsg.getString("and") + " " + resPageMsg.getString("RESPONSE_VALUES_column") + " " + resPageMsg.getString("at_row") + k + " " + resPageMsg.getString("items_worksheet") + "; " + resPageMsg.getString("perhaps_missing_comma"));
htmlErrors.put(j + ", " + k + ", 14", resPageMsg.getString("number_option_not_match"));
htmlErrors.put(j + ", " + k + ", 15", resPageMsg.getString("number_value_not_match"));
}
}
cell = sheet.getRow(k).getCell((short) 16);
String dataType = getValue(cell);
dataType = dataType.replaceAll("<[^>]*>", "");
String dataTypeIdString = "1";
if (StringUtil.isBlank(dataType)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("DATA_TYPE_column") + " " + resPageMsg.getString("was_blank_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet"));
htmlErrors.put(j + ", " + k + ", 16", resPageMsg.getString("required_field"));
} else {
if (!ItemDataType.findByName(dataType.toLowerCase())) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("DATA_TYPE_column") + " " + resPageMsg.getString("was_invalid_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + ", " + k + ", 16", resPageMsg.getString("INVALID_FIELD"));
} else {
if ("file".equalsIgnoreCase(responseType) && !"FILE".equalsIgnoreCase(dataType)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("DATA_TYPE_column") + " " + resPageMsg.getString("should_be_file") + " " + resPageMsg.getString("at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + ", " + k + ", 16", resPageMsg.getString("should_be_file"));
}
// dataTypeId =
// (ItemDataType.getByName(dataType)).getId();
dataTypeIdString = "(SELECT ITEM_DATA_TYPE_ID From ITEM_DATA_TYPE Where CODE='" + dataType.toUpperCase() + "')";
}
}
if (responseTypeId == 3 || responseTypeId == 5 || responseTypeId == 6 || responseTypeId == 7) {
// make sure same responseLabels have same datatype
if (labelWithType.containsKey(responseLabel)) {
logger.debug("in label=" + responseLabel);
if (!dataType.equalsIgnoreCase(labelWithType.get(responseLabel).toString())) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("DATA_TYPE_column") + " " + resPageMsg.getString("does_not_match_the_item_data_type_with_the_same_response_label") + " " + k + ", " + resPageMsg.getString("items_worksheet"));
htmlErrors.put(j + "," + k + ",16", resPageMsg.getString("INVALID_FIELD"));
}
} else {
labelWithType.put(responseLabel, dataType);
// make sure response values matching datatype
if (resValArray.length > 0) {
boolean wrongType = false;
if ("int".equalsIgnoreCase(dataType)) {
for (String s : resValArray) {
String st = s != null && s.length() > 0 ? s.trim() : "";
if (st.length() > 0) {
try {
Integer I = Integer.parseInt(s.trim());
// but 2.3 is not integer
if (!I.toString().equals(s.trim())) {
wrongType = true;
}
} catch (Exception e) {
wrongType = true;
}
}
}
if (wrongType) {
wrongType = false;
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("RESPONSE_VALUES_column") + " " + resPageMsg.getString("should_be_integer") + " " + resPageMsg.getString("at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + ", " + k + ", 15", resPageMsg.getString("should_be_integer"));
}
} else if ("real".equalsIgnoreCase(dataType)) {
for (String s : resValArray) {
String st = s != null && s.length() > 0 ? s.trim() : "";
if (st.length() > 0) {
try {
Double I = Double.parseDouble(s.trim());
} catch (Exception e) {
wrongType = true;
}
}
}
if (wrongType) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("RESPONSE_VALUES_column") + " " + resPageMsg.getString("should_be_real") + " " + resPageMsg.getString("at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ".");
htmlErrors.put(j + ", " + k + ", 15", resPageMsg.getString("should_be_real"));
}
}
}
}
}
cell = sheet.getRow(k).getCell((short) 17);
String regexp = getValue(cell);
String regexp1 = "";
if (!StringUtil.isBlank(regexp)) {
// parse the string and get reg exp eg. regexp:
// /[0-9]*/
regexp1 = regexp.trim();
if (regexp1.startsWith("regexp:")) {
String finalRegexp = regexp1.substring(7).trim();
if (finalRegexp.contains("\\\\")) {
// \\ in the regular expression it should
// not be allowed
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("VALIDATION_column") + " " + resPageMsg.getString("has_an_invalid_regular_expression_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ". " + resPageMsg.getString("regular_expression_contained") + " '\\\\', " + resPageMsg.getString("it_should_only_contain_one") + "'\\'. ");
htmlErrors.put(j + "," + k + ",17", resPageMsg.getString("INVALID_FIELD"));
} else {
if (finalRegexp.startsWith("/") && finalRegexp.endsWith("/")) {
finalRegexp = finalRegexp.substring(1, finalRegexp.length() - 1);
try {
Pattern p = Pattern.compile(finalRegexp);
// YW 11-21-2007 << add another \ if
// there is \ in regexp
char[] chars = regexp1.toCharArray();
regexp1 = "";
for (char c : chars) {
if (c == '\\' && !dbName.equals("oracle")) {
regexp1 += c + "\\";
} else {
regexp1 += c;
}
}
// YW >>
} catch (PatternSyntaxException pse) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("VALIDATION_column") + resPageMsg.getString("has_an_invalid_regular_expression_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ". " + resPageMsg.getString("Example:") + " regexp: /[0-9]*/ ");
htmlErrors.put(j + "," + k + ",17", resPageMsg.getString("INVALID_FIELD"));
}
} else {
// errors.add("The VALIDATION column has
// an invalid regular expression at row
// " + k
// + ", Items worksheet. Example:
// regexp: /[0-9]*/ ");
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("VALIDATION_column") + " " + resPageMsg.getString("has_an_invalid_regular_expression_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ". " + resPageMsg.getString("Example") + " regexp: /[0-9]*/ ");
htmlErrors.put(j + "," + k + ",17", resPageMsg.getString("INVALID_FIELD"));
}
}
} else if (regexp1.startsWith("func:")) {
boolean isProperFunction = false;
try {
Validator.processCRFValidationFunction(regexp1);
isProperFunction = true;
} catch (Exception e) {
errors.add(e.getMessage() + ", " + resPageMsg.getString("at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ". ");
htmlErrors.put(j + "," + k + ",17", resPageMsg.getString("INVALID_FIELD"));
}
} else {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("VALIDATION_column") + " " + resPageMsg.getString("was_invalid_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ". ");
htmlErrors.put(j + "," + k + ",17", resPageMsg.getString("INVALID_FIELD"));
}
}
cell = sheet.getRow(k).getCell((short) 18);
String regexpError = getValue(cell);
regexpError = regexpError.replaceAll("<[^>]*>", "");
if (!StringUtil.isBlank(regexp) && StringUtil.isBlank(regexpError)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("VALIDATION_ERROR_MESSAGE_column") + resPageMsg.getString("was_blank_at_row") + k + ", " + resPageMsg.getString("items_worksheet") + ". " + resPageMsg.getString("cannot_be_blank_if_VALIDATION_not_blank"));
htmlErrors.put(j + "," + k + ",18", resPageMsg.getString("required_field"));
}
if (regexpError != null && regexpError.length() > 255) {
errors.add(resPageMsg.getString("regexp_errror_length_error"));
}
boolean phiBoolean = false;
cell = sheet.getRow(k).getCell((short) 19);
// String phi = getValue(cell);
String phi = "";
if (cell.getCellType() == HSSFCell.CELL_TYPE_NUMERIC) {
double dphi = cell.getNumericCellValue();
if ((dphi - (int) dphi) * 1000 == 0) {
phi = (int) dphi + "";
}
}
if (!"0".equals(phi) && !"1".equals(phi)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("PHI_column") + resPageMsg.getString("was_invalid_at_row") + k + ", " + resPageMsg.getString("items_worksheet") + ". " + resPageMsg.getString("PHI_column") + " " + resPageMsg.getString("can_only_be_either_0_or_1"));
htmlErrors.put(j + "," + k + ",19", resPageMsg.getString("INVALID_VALUE"));
} else {
phiBoolean = "1".equals(phi) ? true : false;
}
boolean isRequired = false;
cell = sheet.getRow(k).getCell((short) 20);
String required = getValue(cell);
logger.info(getValue(cell));
// String required = "";
if (StringUtil.isBlank(required)) {
required = "0";
} else if (cell.getCellType() == HSSFCell.CELL_TYPE_NUMERIC) {
double dr = cell.getNumericCellValue();
if ((dr - (int) dr) * 1000 == 0) {
required = (int) dr + "";
}
}
if (!"0".equals(required) && !"1".equals(required)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("REQUIRED_column") + " " + resPageMsg.getString("was_invalid_at_row") + " " + k + ", " + resPageMsg.getString("items_worksheet") + ". " + resPageMsg.getString("REQUIRED_column") + resPageMsg.getString("can_only_be_either_0_or_1"));
htmlErrors.put(j + "," + k + ",20", resPageMsg.getString("INVALID_VALUE"));
} else {
isRequired = "1".equals(required) ? true : false;
}
// Create oid for Item Bean
String itemOid = idao.getValidOid(new ItemBean(), crfName, itemName, itemOids);
itemOids.add(itemOid);
// better spot for checking item might be right here,
// tbh 7-25
String vlSql = "";
ArrayList<SqlParameter> sqlParameters = new ArrayList<>();
QueryObject qo = new QueryObject();
if (dbName.equals("oracle")) {
/* vlSql =
"INSERT INTO ITEM (NAME,DESCRIPTION,UNITS,PHI_STATUS,"
+ "ITEM_DATA_TYPE_ID, ITEM_REFERENCE_TYPE_ID,STATUS_ID,OWNER_ID,DATE_CREATED,OC_OID) " + "VALUES ('"
+ stripQuotes(itemName) + "','" + stripQuotes(descLabel) + "','" + stripQuotes(unit) + "'," + (phiBoolean == true ? 1 : 0)
+ "," + dataTypeIdString + ",1,1," + ub.getId() + ", sysdate" + ",'" + itemOid + "')";*/
vlSql = "INSERT INTO ITEM (NAME,DESCRIPTION,UNITS,PHI_STATUS," + "ITEM_DATA_TYPE_ID, ITEM_REFERENCE_TYPE_ID,STATUS_ID,OWNER_ID,DATE_CREATED,OC_OID) " + "VALUES (?,?,?," + (phiBoolean == true ? 1 : 0) + "," + dataTypeIdString + ",1,1," + ub.getId() + ", sysdate" + ",?)";
} else {
/*vlSql =
"INSERT INTO ITEM (NAME,DESCRIPTION,UNITS,PHI_STATUS,"
+ "ITEM_DATA_TYPE_ID, ITEM_REFERENCE_TYPE_ID,STATUS_ID,OWNER_ID,DATE_CREATED,OC_OID) " + "VALUES ('"
+ stripQuotes(itemName) + "','" + stripQuotes(descLabel) + "','" + stripQuotes(unit) + "'," + phiBoolean + ","
+ dataTypeIdString + ",1,1," + ub.getId() + ", NOW()" + ",'" + itemOid + "')";*/
vlSql = "INSERT INTO ITEM (NAME,DESCRIPTION,UNITS,PHI_STATUS," + "ITEM_DATA_TYPE_ID, ITEM_REFERENCE_TYPE_ID,STATUS_ID,OWNER_ID,DATE_CREATED,OC_OID) " + "VALUES (?, ?, ?," + phiBoolean + "," + dataTypeIdString + ",1,1," + ub.getId() + ", NOW()" + ",?)";
}
// backupItemQueries.put(itemName, vlSql);
sqlParameters = new ArrayList<>();
sqlParameters.add(new SqlParameter(itemName));
sqlParameters.add(new SqlParameter(descLabel));
sqlParameters.add(new SqlParameter(unit));
sqlParameters.add(new SqlParameter(itemOid));
qo = new QueryObject();
qo.setSql(vlSql);
qo.setSqlParameters(sqlParameters);
backupItemQueries.put(itemName, qo);
// to compare items from DB later, if two items have the
// same name,
// but different units or phiStatus, they are different
ItemBean ib = new ItemBean();
ib.setName(itemName);
ib.setUnits(unit);
ib.setPhiStatus(phiBoolean);
ib.setDescription(descLabel);
ib.setDataType(ItemDataType.getByName(dataType.toLowerCase()));
// put metadata into item
ResponseSetBean rsb = new ResponseSetBean();
// notice that still "\\," in options - jxu-08-31-06
String updatedResOptions = resOptions.replaceAll("\\\\,", "\\,");
String updatedResValues = resValues.replaceAll("\\\\,", "\\,");
// following rsb used in isResponseValid in CreateCRFVersionServlet for comparing response
// options text and values between form versions. Please keep as is. - Z 19-Jun-2020
rsb.setOptions(stripQuotes(updatedResOptions), stripQuotes(updatedResValues));
ItemFormMetadataBean ifmb = new ItemFormMetadataBean();
ifmb.setResponseSet(rsb);
ib.setItemMeta(ifmb);
items.put(itemName, ib);
int ownerId = ub.getId();
if (!itemCheck.containsKey(itemName)) {
// item not in
// the DB
// openQueries.put(itemName, vlSql);
openQueries.put(itemName, qo);
} else {
// item in the DB
ItemBean oldItem = (ItemBean) idao.findByNameAndCRFId(itemName, crfId);
if (oldItem.getOwnerId() == ub.getId()) {
// update
if (!cvdao.hasItemData(oldItem.getId())) {
// no
// item
// data
String upSql = "";
if (dbName.equals("oracle")) {
/* upSql =
"UPDATE ITEM SET DESCRIPTION='" + stripQuotes(descLabel) + "'," + "UNITS='" + stripQuotes(unit) + "',"
+ "PHI_STATUS=" + (phiBoolean ? 1 : 0) + "," + "ITEM_DATA_TYPE_ID=" + dataTypeIdString
+ " WHERE exists (SELECT versioning_map.item_id from versioning_map, crf_version where"
+ " versioning_map.crf_version_id = crf_version.crf_version_id" + " AND crf_version.crf_id= " + crfId
+ " AND item.item_id = versioning_map.item_id)" + " AND item.name='" + stripQuotes(itemName)
+ "' AND item.owner_id = " + ownerId;*/
upSql = "UPDATE ITEM SET DESCRIPTION= ?,UNITS= ?, " + "PHI_STATUS=" + (phiBoolean ? 1 : 0) + "," + "ITEM_DATA_TYPE_ID=" + dataTypeIdString + " WHERE exists (SELECT versioning_map.item_id from versioning_map, crf_version where" + " versioning_map.crf_version_id = crf_version.crf_version_id AND crf_version.crf_id= " + crfId + " AND item.item_id = versioning_map.item_id) AND item.name= ? " + "' AND item.owner_id = ?";
} else {
/* upSql =
"UPDATE ITEM SET DESCRIPTION='" + stripQuotes(descLabel) + "'," + "UNITS='" + stripQuotes(unit) + "',"
+ "PHI_STATUS=" + phiBoolean + "," + "ITEM_DATA_TYPE_ID=" + dataTypeIdString
+ " FROM versioning_map, crf_version" + " WHERE item.name='" + stripQuotes(itemName) + "' AND item.owner_id = "
+ ownerId + " AND item.item_id = versioning_map.item_id AND"
+ " versioning_map.crf_version_id = crf_version.crf_version_id" + " AND crf_version.crf_id = " + crfId;*/
upSql = "UPDATE ITEM SET DESCRIPTION= ?, UNITS= ?," + "PHI_STATUS=" + phiBoolean + "," + "ITEM_DATA_TYPE_ID=" + dataTypeIdString + " FROM versioning_map, crf_version" + " WHERE item.name= ? AND item.owner_id =? " + " AND item.item_id = versioning_map.item_id AND" + " versioning_map.crf_version_id = crf_version.crf_version_id" + " AND crf_version.crf_id = " + crfId;
}
// end of if dbname
// openQueries.put(itemName, upSql);
sqlParameters = new ArrayList<>();
sqlParameters.add(new SqlParameter(descLabel));
sqlParameters.add(new SqlParameter(unit));
sqlParameters.add(new SqlParameter(itemName));
sqlParameters.add(new SqlParameter(ownerId + "", JDBCType.INTEGER));
qo = new QueryObject();
qo.setSql(upSql);
qo.setSqlParameters(sqlParameters);
openQueries.put(itemName, qo);
} else {
String upSql = "";
if (dbName.equals("oracle")) {
upSql = "UPDATE ITEM SET DESCRIPTION= ?," + "PHI_STATUS=" + (phiBoolean ? 1 : 0) + " WHERE exists (SELECT versioning_map.item_id from versioning_map, crf_version where" + " versioning_map.crf_version_id = crf_version.crf_version_id" + " AND crf_version.crf_id= " + crfId + " AND item.item_id = versioning_map.item_id)" + " AND item.name= ? " + " AND item.owner_id = ?";
} else {
upSql = "UPDATE ITEM SET DESCRIPTION= ?," + "PHI_STATUS=" + phiBoolean + " FROM versioning_map, crf_version" + " WHERE item.name= ? AND item.owner_id = ? " + ownerId + " AND item.item_id = versioning_map.item_id AND " + " versioning_map.crf_version_id = crf_version.crf_version_id" + " AND crf_version.crf_id = " + crfId;
}
// end of if dbName
// openQueries.put(itemName, upSql);
sqlParameters = new ArrayList<>();
sqlParameters.add(new SqlParameter(descLabel));
sqlParameters.add(new SqlParameter(itemName));
sqlParameters.add(new SqlParameter(ownerId + "", JDBCType.INTEGER));
qo = new QueryObject();
qo.setSql(upSql);
qo.setSqlParameters(sqlParameters);
openQueries.put(itemName, qo);
}
} else {
ownerId = oldItem.getOwner().getId();
}
}
String sql = "";
sqlParameters = new ArrayList<>();
if (dbName.equals("oracle")) {
// resOptions = resOptions.replaceAll("\\\\,",
// "\\,");
/* sql =
"INSERT INTO RESPONSE_SET (LABEL, OPTIONS_TEXT, OPTIONS_VALUES, " + "RESPONSE_TYPE_ID, VERSION_ID)" + " VALUES ('"
+ stripQuotes(responseLabel) + "', '" + stripQuotes(resOptions.replaceAll("\\\\,", "\\,")) + "','"
+ stripQuotes(resValues.replace("\\\\", "\\")) + "'," + "(SELECT RESPONSE_TYPE_ID From RESPONSE_TYPE Where NAME='"
+ stripQuotes(responseType.toLowerCase()) + "')," + versionIdString + ")";*/
sql = "INSERT INTO RESPONSE_SET (LABEL, OPTIONS_TEXT, OPTIONS_VALUES, RESPONSE_TYPE_ID, VERSION_ID)" + " VALUES (?, ?, ?,(SELECT RESPONSE_TYPE_ID From RESPONSE_TYPE Where NAME=?)," + versionIdString + ")";
sqlParameters.add(new SqlParameter(responseLabel));
sqlParameters.add(new SqlParameter(resOptions.replaceAll("\\\\,", "\\,")));
sqlParameters.add(new SqlParameter(resValues.replace("\\\\", "\\")));
sqlParameters.add(new SqlParameter(responseType.toLowerCase()));
// in versionIdString there is one parameter:crfId
sqlParameters.add(new SqlParameter(crfId + "", JDBCType.INTEGER));
} else {
/* sql =
"INSERT INTO RESPONSE_SET (LABEL, OPTIONS_TEXT, OPTIONS_VALUES, " + "RESPONSE_TYPE_ID, VERSION_ID)" + " VALUES ('"
+ stripQuotes(responseLabel) + "', E'" + stripQuotes(resOptions) + "', E'" + stripQuotes(resValues) + "',"
+ "(SELECT RESPONSE_TYPE_ID From RESPONSE_TYPE Where NAME='" + stripQuotes(responseType.toLowerCase()) + "'),"
+ versionIdString + ")";*/
sql = "INSERT INTO RESPONSE_SET (LABEL, OPTIONS_TEXT, OPTIONS_VALUES, RESPONSE_TYPE_ID, VERSION_ID)" + " VALUES (?, ?, ?,(SELECT RESPONSE_TYPE_ID From RESPONSE_TYPE Where NAME=?)," + versionIdString + ")";
sqlParameters.add(new SqlParameter(responseLabel));
sqlParameters.add(new SqlParameter(updatedResOptions));
sqlParameters.add(new SqlParameter(updatedResValues));
sqlParameters.add(new SqlParameter(responseType.toLowerCase()));
// in versionIdString there is one parameter:crfId
sqlParameters.add(new SqlParameter(crfId + "", JDBCType.INTEGER));
}
if (!resNames.contains(responseLabel)) {
qo = new QueryObject();
qo.setSql(sql);
qo.setSqlParameters(sqlParameters);
queries.add(qo);
resNames.add(responseLabel);
// this will have to change since we have some data
// in the actual
// spreadsheet
// change it to caching response set names in a
// collection?
// or just delete the offending cells from the
// spreadsheet?
}
String parentItemString = "0";
if (!StringUtil.isBlank(parentItem)) {
if (dbName.equals("oracle")) {
parentItemString = "(SELECT MAX(ITEM_ID) FROM ITEM WHERE NAME='" + parentItem + "' AND owner_id = " + ownerId + " )";
} else {
parentItemString = "(SELECT ITEM_ID FROM ITEM WHERE NAME='" + parentItem + "' AND owner_id = " + ownerId + " ORDER BY OC_OID DESC LIMIT 1)";
}
}
String selectCorrectItemQueryPostgres = " (SELECT I.ITEM_ID FROM ITEM I LEFT OUTER JOIN ITEM_FORM_METADATA IFM ON I.ITEM_Id = IFM.ITEM_ID LEFT OUTER JOIN CRF_VERSION CV ON IFM.CRF_VERSION_ID = CV.CRF_VERSION_ID WHERE " + " ( I.NAME='" + itemName + "'" + " AND I.owner_id = " + ownerId + " AND CV.CRF_VERSION_ID is null )" + " OR " + " ( I.NAME='" + itemName + "'" + " AND I.owner_id = " + ownerId + " AND CV.CRF_VERSION_ID is not null AND CV.CRF_ID =" + crfId + " ) " + " ORDER BY I.OC_ID DESC LIMIT 1) ";
String selectCorrectItemQueryOracle = " (SELECT MAX(I.ITEM_ID) FROM ITEM I LEFT OUTER JOIN ITEM_FORM_METADATA IFM ON I.ITEM_Id = IFM.ITEM_ID LEFT OUTER JOIN CRF_VERSION CV ON IFM.CRF_VERSION_ID = CV.CRF_VERSION_ID WHERE " + " ( I.NAME='" + itemName + "'" + " AND I.owner_id = " + ownerId + " AND CV.CRF_VERSION_ID is null )" + " OR " + " ( I.NAME='" + itemName + "'" + " AND I.owner_id = " + ownerId + " AND CV.CRF_VERSION_ID is not null AND CV.CRF_ID =" + crfId + " )) ";
String sql2 = "";
sqlParameters = new ArrayList<>();
if (dbName.equals("oracle")) {
/* sql2 =
"INSERT INTO ITEM_FORM_METADATA (CRF_VERSION_ID, RESPONSE_SET_ID," + "ITEM_ID,SUBHEADER,header,LEFT_ITEM_TEXT,"
+ "RIGHT_ITEM_TEXT,PARENT_ID,SECTION_ID,ORDINAL,PARENT_LABEL,COLUMN_NUMBER,PAGE_NUMBER_LABEL,question_number_label,"
+ "REGEXP,REGEXP_ERROR_MSG,REQUIRED)" + " VALUES ("
+ versionIdString
+ ",(SELECT RESPONSE_SET_ID FROM RESPONSE_SET WHERE LABEL='"
+ stripQuotes(responseLabel)
+ "'"
+ " AND VERSION_ID="
+ versionIdString
+ "),"
+ selectCorrectItemQueryOracle
+ ",'"
+ stripQuotes(subHeader)
+ "','"
+ stripQuotes(header)
+ "','"
+ stripQuotes(leftItemText)
+ "','"
+ stripQuotes(rightItemText)
+ "',"
+ parentItemString
+ ", (SELECT SECTION_ID FROM SECTION WHERE LABEL='"
+ secName
+ "' AND "
+ "CRF_VERSION_ID IN "
+ versionIdString
+ "), "
+ k
+ ",'"
+ parentItem
+ "',"
+ columnNum
+ ",'"
+ stripQuotes(page)
+ "','"
+ stripQuotes(questionNum)
+ "','"
+ stripQuotes(regexp1) + "','" + stripQuotes(regexpError) + "', " + (isRequired ? 1 : 0) + ")";
*/
sql2 = "INSERT INTO ITEM_FORM_METADATA (CRF_VERSION_ID, RESPONSE_SET_ID," + "ITEM_ID,SUBHEADER,header,LEFT_ITEM_TEXT," + "RIGHT_ITEM_TEXT,PARENT_ID,SECTION_ID,ORDINAL,PARENT_LABEL,COLUMN_NUMBER,PAGE_NUMBER_LABEL,question_number_label," + "REGEXP,REGEXP_ERROR_MSG,REQUIRED)" + " VALUES (" + versionIdString + // responseLabel
",(SELECT RESPONSE_SET_ID FROM RESPONSE_SET WHERE LABEL=?" + " AND VERSION_ID=" + versionIdString + ")," + selectCorrectItemQueryPostgres + // subHeader, header, leftItemText, rightItemText
",?, ?, ?, ?, " + parentItemString + ", (SELECT SECTION_ID FROM SECTION WHERE LABEL='" + secName + "' AND " + "CRF_VERSION_ID IN " + versionIdString + "), " + k + ",'" + parentItem + "'," + columnNum + // page, questionNum, regexp1, regexpError
",?,?,?,?, " + (isRequired ? 1 : 0) + ")";
} else {
/* sql2 =
"INSERT INTO ITEM_FORM_METADATA (CRF_VERSION_ID, RESPONSE_SET_ID," + "ITEM_ID,SUBHEADER,HEADER,LEFT_ITEM_TEXT,"
+ "RIGHT_ITEM_TEXT,PARENT_ID,SECTION_ID,ORDINAL,PARENT_LABEL,COLUMN_NUMBER,PAGE_NUMBER_LABEL,question_number_label,"
+ "REGEXP,REGEXP_ERROR_MSG,REQUIRED)" + " VALUES ("
+ versionIdString
+ ",(SELECT RESPONSE_SET_ID FROM RESPONSE_SET WHERE LABEL='"
+ stripQuotes(responseLabel)
+ "'"
+ " AND VERSION_ID="
+ versionIdString
+ "),"
+ selectCorrectItemQueryPostgres
+ ",'"
+ stripQuotes(subHeader)
+ "','"
+ stripQuotes(header)
+ "','"
+ stripQuotes(leftItemText)
+ "','"
+ stripQuotes(rightItemText)
+ "',"
+ parentItemString
+ ", (SELECT SECTION_ID FROM SECTION WHERE LABEL='"
+ secName
+ "' AND "
+ "CRF_VERSION_ID IN "
+ versionIdString
+ "), "
+ k
+ ",'"
+ parentItem
+ "',"
+ columnNum
+ ",'"
+ stripQuotes(page)
+ "','"
+ stripQuotes(questionNum)
+ "','"
+ stripQuotes(regexp1) + "','" + stripQuotes(regexpError) + "', " + isRequired + ")";*/
sql2 = "INSERT INTO ITEM_FORM_METADATA (CRF_VERSION_ID, RESPONSE_SET_ID," + "ITEM_ID,SUBHEADER,HEADER,LEFT_ITEM_TEXT," + "RIGHT_ITEM_TEXT,PARENT_ID,SECTION_ID,ORDINAL,PARENT_LABEL,COLUMN_NUMBER,PAGE_NUMBER_LABEL,question_number_label," + "REGEXP,REGEXP_ERROR_MSG,REQUIRED)" + " VALUES (" + versionIdString + // responseLabel
",(SELECT RESPONSE_SET_ID FROM RESPONSE_SET WHERE LABEL=?" + " AND VERSION_ID=" + versionIdString + ")," + selectCorrectItemQueryPostgres + // subHeader, header, leftItemText, rightItemText
",?, ?, ?, ?, " + parentItemString + ", (SELECT SECTION_ID FROM SECTION WHERE LABEL='" + secName + "' AND " + "CRF_VERSION_ID IN " + versionIdString + "), " + k + ",'" + parentItem + "'," + columnNum + // page, questionNum, regexp1, regexpError
",?,?,?,?, " + isRequired + ")";
}
// in versionIdString there one parameter:crfId
sqlParameters.add(new SqlParameter(crfId + "", JDBCType.INTEGER));
sqlParameters.add(new SqlParameter(responseLabel));
sqlParameters.add(new SqlParameter(crfId + "", JDBCType.INTEGER));
sqlParameters.add(new SqlParameter(subHeader));
sqlParameters.add(new SqlParameter(header));
sqlParameters.add(new SqlParameter(leftItemText));
sqlParameters.add(new SqlParameter(rightItemText));
// in versionIdString there one parameter:crfId
sqlParameters.add(new SqlParameter(crfId + "", JDBCType.INTEGER));
sqlParameters.add(new SqlParameter(page));
sqlParameters.add(new SqlParameter(questionNum));
sqlParameters.add(new SqlParameter(regexp1));
sqlParameters.add(new SqlParameter(regexpError));
qo = new QueryObject();
qo.setSql(sql2);
qo.setSqlParameters(sqlParameters);
queries.add(qo);
// link version with items now
String sql3 = "";
if (dbName.equals("oracle")) {
sql3 = "INSERT INTO VERSIONING_MAP (CRF_VERSION_ID, ITEM_ID) VALUES ( " + versionIdString + "," + selectCorrectItemQueryOracle + ")";
} else {
sql3 = "INSERT INTO VERSIONING_MAP (CRF_VERSION_ID, ITEM_ID) VALUES ( " + versionIdString + "," + selectCorrectItemQueryPostgres + ")";
}
sqlParameters = new ArrayList<>();
// in versionIdString there one parameter:crfId
sqlParameters.add(new SqlParameter(crfId + "", JDBCType.INTEGER));
qo = new QueryObject();
qo.setSql(sql3);
qo.setSqlParameters(sqlParameters);
queries.add(qo);
// this item doesn't have group, so put it into
// 'Ungrouped' group
String sqlGroupLabel = "";
if (dbName.equals("oracle")) {
sqlGroupLabel = "INSERT INTO ITEM_GROUP_METADATA (" + "item_group_id,header," + "subheader, layout, repeat_number, repeat_max," + " repeat_array,row_start_number, crf_version_id," + "item_id , ordinal, borders) VALUES (" + "(SELECT MAX(ITEM_GROUP_ID) FROM ITEM_GROUP WHERE NAME='Ungrouped' AND crf_id = " + crfId + " ),'" + "" + "', '" + "" + "', '" + "" + "', " + 1 + ", " + 1 + ", '', 1," + versionIdString + "," + // + itemName + "' ),"
"(SELECT MAX(ITEM.ITEM_ID) FROM ITEM,ITEM_FORM_METADATA,CRF_VERSION WHERE ITEM.NAME='" + itemName + "' " + "AND ITEM.ITEM_ID = ITEM_FORM_METADATA.ITEM_ID and ITEM_FORM_METADATA.CRF_VERSION_ID=CRF_VERSION.CRF_VERSION_ID " + "AND CRF_VERSION.CRF_ID= " + crfId + " )," + k + ",0)";
} else {
sqlGroupLabel = "INSERT INTO ITEM_GROUP_METADATA (" + "item_group_id,HEADER," + "subheader, layout, repeat_number, repeat_max," + " repeat_array,row_start_number, crf_version_id," + "item_id , ordinal, borders) VALUES (" + "(SELECT ITEM_GROUP_ID FROM ITEM_GROUP WHERE NAME='Ungrouped' AND crf_id = " + crfId + " ORDER BY oc_oid DESC LIMIT 1),'" + "" + "', '" + "" + "', '" + "" + "', " + 1 + ", " + 1 + ", '', 1," + versionIdString + "," + // LIMIT 1),"
"(SELECT ITEM.ITEM_ID FROM ITEM,ITEM_FORM_METADATA,CRF_VERSION WHERE ITEM.NAME='" + itemName + "' " + "AND ITEM.ITEM_ID = ITEM_FORM_METADATA.ITEM_ID and ITEM_FORM_METADATA.CRF_VERSION_ID=CRF_VERSION.CRF_VERSION_ID " + "AND CRF_VERSION.CRF_ID= " + crfId + " ORDER BY ITEM.OC_OID DESC LIMIT 1)," + k + ",0)";
}
sqlParameters = new ArrayList<>();
// in versionIdString there one parameter:crfId
sqlParameters.add(new SqlParameter(crfId + "", JDBCType.INTEGER));
qo = new QueryObject();
qo.setSql(sqlGroupLabel);
qo.setSqlParameters(sqlParameters);
queries.add(qo);
}
} else if (sheetName.equalsIgnoreCase("Sections")) {
logger.info("read sections");
// multiple rows, six cells, last one is number
for (int k = 1; k < numRows; k++) {
if (blankRowCount == 5) {
logger.info("hit end of the row ");
break;
}
if (sheet.getRow(k) == null) {
blankRowCount++;
continue;
}
HSSFCell cell = sheet.getRow(k).getCell((short) 0);
String secLabel = getValue(cell);
secLabel = secLabel.replaceAll("<[^>]*>", "");
if (StringUtil.isBlank(secLabel)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("SECTION_LABEL_column") + " " + resPageMsg.getString("was_blank_at_row") + k + " " + ", " + resPageMsg.getString("sections_worksheet") + ".");
htmlErrors.put(j + "," + k + ",0", resPageMsg.getString("required_field"));
}
if (secLabel != null && secLabel.length() > 2000) {
errors.add(resPageMsg.getString("section_label_length_error"));
}
if (secLabel.contains("'")) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("SECTION_LABEL_column") + " value " + secLabel + " " + resPageMsg.getString("has_invalid_character") + "\" ' \"" + ". " + resPageMsg.getString("remove_invalid_character"));
}
if (secNames.contains(secLabel)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("SECTION_LABEL_column") + resPageMsg.getString("was_a_duplicate_of") + secLabel + " " + resPageMsg.getString("at_row") + " " + k + ", " + resPageMsg.getString("sections_worksheet") + ".");
htmlErrors.put(j + "," + k + ",0", resPageMsg.getString("DUPLICATE_FIELD"));
}
// logger.info("section name:" + secLabel + "row num:"
// +k);
secNames.add(secLabel);
cell = sheet.getRow(k).getCell((short) 1);
String title = getValue(cell);
title = title.replaceAll("<[^>]*>", "");
if (StringUtil.isBlank(title)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("SECTION_TITLE_column") + " " + resPageMsg.getString("was_blank_at_row") + " " + k + ", " + resPageMsg.getString("sections_worksheet") + ".");
htmlErrors.put(j + "," + k + ",1", resPageMsg.getString("required_field"));
}
if (title != null && title.length() > 2000) {
errors.add(resPageMsg.getString("section_title_length_error"));
}
cell = sheet.getRow(k).getCell((short) 2);
String subtitle = getValue(cell);
if (subtitle != null && subtitle.length() > 2000) {
errors.add(resPageMsg.getString("section_subtitle_length_error"));
}
cell = sheet.getRow(k).getCell((short) 3);
String instructions = getValue(cell);
if (instructions != null && instructions.length() > 2000) {
errors.add(resPageMsg.getString("section_instruction_length_error"));
}
cell = sheet.getRow(k).getCell((short) 4);
String pageNumber = getValue(cell);
if (pageNumber != null && pageNumber.length() > 5) {
errors.add(resPageMsg.getString("section_page_number_length_error"));
}
cell = sheet.getRow(k).getCell((short) 5);
String parentSection = getValue(cell);
parentSection = parentSection.replaceAll("<[^>]*>", "");
if (!StringUtil.isBlank(parentSection)) {
try {
parentId = Integer.parseInt(parentSection);
} catch (NumberFormatException ne) {
parentId = 0;
}
}
String sql = "";
if (dbName.equals("oracle")) {
/* sql =
"INSERT INTO SECTION (CRF_VERSION_ID," + "STATUS_ID,LABEL, TITLE, INSTRUCTIONS, SUBTITLE, PAGE_NUMBER_LABEL,"
+ "ORDINAL, PARENT_ID, OWNER_ID, DATE_CREATED) " + "VALUES (" + versionIdString + ",1,'" + secLabel + "','"
+ stripQuotes(title) + "', '" + stripQuotes(instructions) + "', '" + stripQuotes(subtitle) + "','" + pageNumber + "'," + k
+ "," + parentId + "," + ub.getId() + ",sysdate)";*/
sql = "INSERT INTO SECTION (CRF_VERSION_ID," + "STATUS_ID,LABEL, TITLE, INSTRUCTIONS, SUBTITLE, PAGE_NUMBER_LABEL," + "ORDINAL, PARENT_ID, OWNER_ID, DATE_CREATED) " + "VALUES (" + versionIdString + ", 1, ? ,?, ?, ?, ?, ?, ?, ?,sysdate)";
} else {
/* sql =
"INSERT INTO SECTION (CRF_VERSION_ID," + "STATUS_ID,LABEL, TITLE, INSTRUCTIONS, SUBTITLE, PAGE_NUMBER_LABEL,"
+ "ORDINAL, PARENT_ID, OWNER_ID, DATE_CREATED) " + "VALUES (" + versionIdString + ",1,'" + secLabel + "','"
+ stripQuotes(title) + "', '" + stripQuotes(instructions) + "', '" + stripQuotes(subtitle) + "','" + pageNumber + "'," + k
+ "," + parentId + "," + ub.getId() + ",NOW())";*/
sql = "INSERT INTO SECTION (CRF_VERSION_ID," + "STATUS_ID,LABEL, TITLE, INSTRUCTIONS, SUBTITLE, PAGE_NUMBER_LABEL," + "ORDINAL, PARENT_ID, OWNER_ID, DATE_CREATED) " + "VALUES (" + versionIdString + ", 1, ? ,?, ?, ?, ?, ?, ?, ?,NOW())";
}
ArrayList<SqlParameter> sqlParameters = new ArrayList<>();
// in versionIdString there one parameter:crfId
sqlParameters.add(new SqlParameter(crfId + "", JDBCType.INTEGER));
sqlParameters.add(new SqlParameter(secLabel));
sqlParameters.add(new SqlParameter(title));
sqlParameters.add(new SqlParameter(instructions));
sqlParameters.add(new SqlParameter(subtitle));
sqlParameters.add(new SqlParameter(pageNumber));
sqlParameters.add(new SqlParameter(k + "", JDBCType.INTEGER));
sqlParameters.add(new SqlParameter(parentId + "", JDBCType.INTEGER));
sqlParameters.add(new SqlParameter(ub.getId() + "", JDBCType.INTEGER));
QueryObject qo = new QueryObject();
qo.setSql(sql);
qo.setSqlParameters(sqlParameters);
queries.add(qo);
}
// end for loop
} else if (sheetName.equalsIgnoreCase("CRF")) {
logger.info("read crf");
// one row, four cells, all strings
if (sheet == null || sheet.getRow(1) == null || sheet.getRow(1).getCell((short) 0) == null) {
throw new CRFReadingException("Blank row found in sheet CRF.");
}
HSSFCell cell = sheet.getRow(1).getCell((short) 0);
crfName = getValue(cell);
crfName = crfName.replaceAll("<[^>]*>", "");
if (StringUtil.isBlank(crfName)) {
// resPageMsg.getString("required_field"));
throw new CRFReadingException("The CRF_NAME column was blank in the CRF worksheet.");
}
if (crfName.length() > 255) {
errors.add(resPageMsg.getString("crf_name_length_error"));
}
CRFBean existingCRFWithSameName = (CRFBean) cdao.findByName(crfName);
if (this.getCrfId() == 0) {
if (existingCRFWithSameName.getName() != null && existingCRFWithSameName.getName().equals(crfName)) {
errors.add(resPageMsg.getString("crf_name_already_used"));
}
}
// TODO Why the following codes are commented out? -jxu
// try {
// CRFBean checkName = (CRFBean) cdao.findByPK(crfId);
// if (!checkName.getName().equals(crfName)) {
// logger.info("crf name is mismatch");
// errors.add(resPageMsg.getString("the") + " " +
// resPageMsg.getString("CRF_NAME_column") +
// resPageMsg.getString("did_not_match_crf_version") + " '"
// + checkName.getName()
// + "' " + resPageMsg.getString("before_you_continue"));
// htmlErrors.put(j + ",1,0",
// resPageMsg.getString("DID_NOT_MATCH_CRF"));
// }
// } catch (Exception pe) {
// logger.warn("Exception happened when check CRF name" +
// pe.getMessage());
// }
cell = sheet.getRow(1).getCell((short) 1);
String version = getValue(cell);
version = version.replaceAll("<[^>]*>", "");
ncrf.setVersionName(version);
if (version != null && version.length() > 255) {
errors.add(resPageMsg.getString("version_length_error"));
}
// YW, 08-22-2007, since versionName is now obtained from
// spreadsheet,
// blank check has been moved to
// CreateCRFVersionServlet.java
// and mismatch check is not necessary
// if (StringUtil.isBlank(version)) {
// errors.add("The VERSION column was blank in the CRF
// worksheet.");
// htmlErrors.put(j + ",1,1", "REQUIRED FIELD");
// }else if (!version.equals(versionName)) {
// errors.add("The VERSION column did not match the intended
// version name "
// + "you want to upload. Make sure this reads '" +
// versionName
// + "' before you continue.");
// htmlErrors.put(j + ",1,1", "DID NOT MATCH VERSION");
// }
cell = sheet.getRow(1).getCell((short) 2);
String versionDesc = getValue(cell);
versionDesc = versionDesc.replaceAll("<[^>]*>", "");
if (versionDesc != null && versionDesc.length() > 4000) {
errors.add(resPageMsg.getString("version_description_length_error"));
}
cell = sheet.getRow(1).getCell((short) 3);
String revisionNotes = getValue(cell);
revisionNotes = revisionNotes.replaceAll("<[^>]*>", "");
if (revisionNotes != null && revisionNotes.length() > 255) {
errors.add(resPageMsg.getString("revision_notes_length_error"));
}
if (StringUtil.isBlank(revisionNotes)) {
errors.add(resPageMsg.getString("the") + " " + resPageMsg.getString("REVISION_NOTES_column") + " " + resPageMsg.getString("was_blank_in_the_CRF_worksheet"));
htmlErrors.put(j + ",1,3", resPageMsg.getString("required_field"));
}
// Generating query string for the new CRF
Connection con = null;
String crfOid = null;
if (crfId == 0) {
crfOid = cdao.getValidOid(new CRFBean(), crfName);
int nextCRFId;
try {
con = ds.getConnection();
/*
* We are selecting the crf id which will be used to
* save the new CRF. Selecting the crf id in advance
* will not cause any problem in a multi threaded
* environment because the nextVal() method always
* returns unique values. So there is no chance of
* processing two CRF simultaneously with same crf
* id.
*/
ResultSet nextIdRs;
if (dbName.equals("oracle")) {
nextIdRs = con.createStatement().executeQuery("select crf_id_seq.nextval from dual");
} else {
nextIdRs = con.createStatement().executeQuery("select nextval('crf_crf_id_seq')");
}
nextIdRs.next();
nextCRFId = nextIdRs.getInt(1);
crfId = nextCRFId;
ncrf.setCrfId(crfId);
String createCRFSql = "";
if (dbName.equals("oracle")) {
/*createCRFSql =
"INSERT INTO CRF (CRF_ID, STATUS_ID, NAME, DESCRIPTION, OWNER_ID, DATE_CREATED, OC_OID, SOURCE_STUDY_ID) VALUES (" + crfId
+ ", 1,'" + stripQuotes(crfName) + "','" + stripQuotes(versionDesc) + "'," + ub.getId() + ",sysdate" + ",'" + crfOid
+ "'," + studyId + ")";*/
createCRFSql = "INSERT INTO CRF (CRF_ID, STATUS_ID, NAME, DESCRIPTION, OWNER_ID, DATE_CREATED, OC_OID, SOURCE_STUDY_ID) VALUES " + "(?, 1, ?, ?, ?, sysdate,? ,?)";
} else {
/* createCRFSql =
"INSERT INTO CRF (CRF_ID, STATUS_ID, NAME, DESCRIPTION, OWNER_ID, DATE_CREATED, OC_OID, SOURCE_STUDY_ID) VALUES (" + crfId
+ ", 1,'" + stripQuotes(crfName) + "','" + stripQuotes(versionDesc) + "'," + ub.getId() + ",NOW()" + ",'" + crfOid
+ "'," + studyId + ")";*/
createCRFSql = "INSERT INTO CRF (CRF_ID, STATUS_ID, NAME, DESCRIPTION, OWNER_ID, DATE_CREATED, OC_OID, SOURCE_STUDY_ID) VALUES " + "(?, 1, ?, ?, ?, NOW(),? ,?)";
}
ArrayList<SqlParameter> sqlParameters = new ArrayList<>();
sqlParameters.add(new SqlParameter(crfId + "", JDBCType.INTEGER));
sqlParameters.add(new SqlParameter(crfName));
sqlParameters.add(new SqlParameter(versionDesc));
sqlParameters.add(new SqlParameter(ub.getId() + "", JDBCType.INTEGER));
sqlParameters.add(new SqlParameter(crfOid));
sqlParameters.add(new SqlParameter(studyId + "", JDBCType.INTEGER));
QueryObject qo = new QueryObject();
qo.setSql(createCRFSql);
qo.setSqlParameters(sqlParameters);
queries.add(qo);
} catch (SQLException e) {
logger.warn("Exception encountered with query select nextval('crf_crf_id_seq'), Message-" + e.getMessage());
} finally {
if (con != null) {
try {
con.close();
} catch (SQLException e) {
logger.warn("Connectin can't be closed");
}
}
}
}
// check for instrument existence here??? tbh 7/28
// engaging in new validation, tbh, 6-4-04
// modify nib.getinstversions to look for version name and
// description
// need to stop uploads of same name-description pairs
HashMap checkCRFVersions = ncrf.getCrfVersions();
// this now returns a hash map of key:version_name
// ->value:version_description
boolean overwrite = false;
if (checkCRFVersions.containsKey(version)) {
logger.info("found a matching version name..." + version);
errors.add(resPageMsg.getString("version_not_unique_cause_confusion"));
htmlErrors.put(j + ",1,2", resPageMsg.getString("NOT_UNIQUE"));
}
// Create oid for Crf Version
String oid;
if (crfOid != null) {
oid = cvdao.getValidOid(new CRFVersionBean(), crfOid, version);
} else {
CRFBean crfBean = (CRFBean) cdao.findByName(crfName);
oid = cvdao.getValidOid(new CRFVersionBean(), crfBean.getOid(), version);
}
String sql = "";
ArrayList<SqlParameter> sqlParameters = new ArrayList<>();
if (dbName.equals("oracle")) {
logger.warn("TEST 2");
if (crfId == 0) {
/*sql =
"INSERT INTO CRF_VERSION (NAME, DESCRIPTION, CRF_ID, STATUS_ID,DATE_CREATED," + "OWNER_ID,REVISION_NOTES,OC_OID) "
+ "VALUES ('" + stripQuotes(version) + "','" + stripQuotes(versionDesc) + "'," + "(SELECT CRF_ID FROM CRF WHERE NAME='"
+ crfName + "'),1,sysdate," + ub.getId() + ",'" + stripQuotes(revisionNotes) + "','" + oid + "')";*/
sql = "INSERT INTO CRF_VERSION (NAME,DESCRIPTION, CRF_ID, STATUS_ID,DATE_CREATED," + "OWNER_ID,REVISION_NOTES,OC_OID) " + "VALUES (?, ?, (SELECT CRF_ID FROM CRF WHERE NAME=?), 1, sysdate, ?, ?, ?)";
sqlParameters.add(new SqlParameter(version + ""));
sqlParameters.add(new SqlParameter(versionDesc));
sqlParameters.add(new SqlParameter(crfName));
sqlParameters.add(new SqlParameter(ub.getId() + "", JDBCType.INTEGER));
sqlParameters.add(new SqlParameter(revisionNotes));
sqlParameters.add(new SqlParameter(oid + ""));
} else {
/* sql =
"INSERT INTO CRF_VERSION (NAME,DESCRIPTION, CRF_ID, STATUS_ID,DATE_CREATED," + "OWNER_ID,REVISION_NOTES,OC_OID) " + "VALUES ('"
+ version + "','" + stripQuotes(versionDesc) + "'," + crfId + ",1,sysdate," + ub.getId() + ",'"
+ stripQuotes(revisionNotes) + "','" + oid + "')";*/
sql = "INSERT INTO CRF_VERSION (NAME,DESCRIPTION, CRF_ID, STATUS_ID,DATE_CREATED," + "OWNER_ID,REVISION_NOTES,OC_OID) " + "VALUES (?, ?, ?, 1, sysdate, ?, ?, ?)";
sqlParameters.add(new SqlParameter(version + ""));
sqlParameters.add(new SqlParameter(versionDesc));
sqlParameters.add(new SqlParameter(crfId + "", JDBCType.INTEGER));
sqlParameters.add(new SqlParameter(ub.getId() + "", JDBCType.INTEGER));
sqlParameters.add(new SqlParameter(revisionNotes));
sqlParameters.add(new SqlParameter(oid + ""));
}
} else {
if (crfId == 0) {
/*sql =
"INSERT INTO CRF_VERSION (NAME, DESCRIPTION, CRF_ID, STATUS_ID,DATE_CREATED," + "OWNER_ID,REVISION_NOTES,OC_OID) "
+ "VALUES ('" + stripQuotes(version) + "','" + stripQuotes(versionDesc) + "'," + "(SELECT CRF_ID FROM CRF WHERE NAME='"
+ crfName + "'),1,NOW()," + ub.getId() + ",'" + stripQuotes(revisionNotes) + "','" + oid + "')";*/
sql = "INSERT INTO CRF_VERSION (NAME,DESCRIPTION, CRF_ID, STATUS_ID,DATE_CREATED," + "OWNER_ID,REVISION_NOTES,OC_OID) " + " VALUES (?, ?, (SELECT CRF_ID FROM CRF WHERE NAME=?), 1, NOW(), ?, ?, ?)";
sqlParameters.add(new SqlParameter(version + ""));
sqlParameters.add(new SqlParameter(versionDesc));
sqlParameters.add(new SqlParameter(crfName));
sqlParameters.add(new SqlParameter(ub.getId() + "", JDBCType.INTEGER));
sqlParameters.add(new SqlParameter(revisionNotes));
sqlParameters.add(new SqlParameter(oid + ""));
} else {
/* sql =
"INSERT INTO CRF_VERSION (NAME,DESCRIPTION, CRF_ID, STATUS_ID,DATE_CREATED," + "OWNER_ID,REVISION_NOTES,OC_OID) " + "VALUES ('"
+ version + "','" + stripQuotes(versionDesc) + "'," + crfId + ",1,NOW()," + ub.getId() + ",'" + stripQuotes(revisionNotes)
+ "','" + oid + "')";*/
sql = "INSERT INTO CRF_VERSION (NAME,DESCRIPTION, CRF_ID, STATUS_ID,DATE_CREATED," + "OWNER_ID,REVISION_NOTES,OC_OID) " + " VALUES (?, ?, ?, 1, NOW(), ?, ?, ?)";
sqlParameters.add(new SqlParameter(version + ""));
sqlParameters.add(new SqlParameter(versionDesc));
sqlParameters.add(new SqlParameter(crfId + "", JDBCType.INTEGER));
sqlParameters.add(new SqlParameter(ub.getId() + "", JDBCType.INTEGER));
sqlParameters.add(new SqlParameter(revisionNotes));
sqlParameters.add(new SqlParameter(oid + ""));
}
}
QueryObject qo = new QueryObject();
qo.setSql(sql);
qo.setSqlParameters(sqlParameters);
queries.add(qo);
for (int i = 0; i < queries.size(); i++) {
String s = (String) queries.get(i);
logger.info("====================" + s);
}
pVersion = version;
pVerDesc = versionDesc;
}
/*versionIdString = "(SELECT CRF_VERSION_ID FROM CRF_VERSION WHERE NAME ='" + pVersion + "' AND CRF_ID=" + crfId + ")";*/
versionIdString = "(SELECT CRF_VERSION_ID FROM CRF_VERSION WHERE NAME ='" + pVersion + "' AND CRF_ID=?)";
// move html creation to here, include error creation as well,
// tbh 7/28
buf.append(sheetName + "<br>");
buf.append("<div class=\"box_T\"><div class=\"box_L\"><div class=\"box_R\"><div class=\"box_B\"><div class=\"box_TL\"><div class=\"box_TR\"><div class=\"box_BL\"><div class=\"box_BR\">");
buf.append("<div class=\"textbox_center\">");
buf.append("<table border=\"0\" cellpadding=\"0\" cellspacing=\"0\" width=\"100%\"");
buf.append("caption=\"" + wb.getSheetName(j) + "\"" + ">");
for (int i = 0; i < numRows; i++) {
buf.append("<tr>");
if (sheet.getRow(i) == null) {
continue;
}
int numCells = sheet.getRow(i).getLastCellNum();
for (int y = 0; y < numCells; y++) {
HSSFCell cell = sheet.getRow(i).getCell((short) y);
int cellType = 0;
String error = " ";
String errorKey = j + "," + i + "," + y;
if (htmlErrors.containsKey(errorKey)) {
error = "<span class=\"alert\">" + htmlErrors.get(errorKey) + "</span>";
}
if (cell == null) {
cellType = HSSFCell.CELL_TYPE_BLANK;
} else {
cellType = cell.getCellType();
}
switch(cellType) {
case HSSFCell.CELL_TYPE_BLANK:
buf.append("<td class=\"table_cell\">" + error + "</td>");
break;
case HSSFCell.CELL_TYPE_NUMERIC:
buf.append("<td class=\"table_cell\">" + cell.getNumericCellValue() + " " + error + "</td>");
break;
case HSSFCell.CELL_TYPE_STRING:
buf.append("<td class=\"table_cell\">" + cell.getStringCellValue() + " " + error + "</td>");
break;
default:
buf.append("<td class=\"table_cell\">" + error + "</td>");
}
}
buf.append("</tr>");
}
buf.append("</table>");
buf.append("<br></div>");
buf.append("</div></div></div></div></div></div></div></div>");
buf.append("</div><br>");
}
// end of the else sheet loop
}
// end of the for loop for sheets
ncrf.setQueries(queries);
ncrf.setItemQueries(openQueries);
ncrf.setBackupItemQueries(backupItemQueries);
ncrf.setItems(items);
if (!errors.isEmpty()) {
ncrf.setErrors(errors);
}
// logger.info("html table:" + buf.toString());
ncrf.setHtmlTable(buf.toString());
return ncrf;
}
Also used :
ItemBean(org.akaza.openclinica.bean.submit.ItemBean)
ItemDAO(org.akaza.openclinica.dao.submit.ItemDAO)
SQLException(java.sql.SQLException)
ItemGroupDAO(org.akaza.openclinica.dao.submit.ItemGroupDAO)
CRFReadingException(org.akaza.openclinica.exception.CRFReadingException)
ItemDataDAO(org.akaza.openclinica.dao.submit.ItemDataDAO)
ResultSet(java.sql.ResultSet)
PatternSyntaxException(java.util.regex.PatternSyntaxException)
Pattern(java.util.regex.Pattern)
CRFDAO(org.akaza.openclinica.dao.admin.CRFDAO)
SqlParameter(org.akaza.openclinica.bean.admin.SqlParameter)
CRFVersionDAO(org.akaza.openclinica.dao.submit.CRFVersionDAO)
Connection(java.sql.Connection)
MeasurementUnitOidGenerator(org.akaza.openclinica.bean.oid.MeasurementUnitOidGenerator)
QueryObject(org.akaza.openclinica.bean.admin.QueryObject)
HSSFWorkbook(org.apache.poi.hssf.usermodel.HSSFWorkbook)
SQLException(java.sql.SQLException)
PatternSyntaxException(java.util.regex.PatternSyntaxException)
CRFReadingException(org.akaza.openclinica.exception.CRFReadingException)
IOException(java.io.IOException)
NewCRFBean(org.akaza.openclinica.bean.admin.NewCRFBean)
CRFBean(org.akaza.openclinica.bean.admin.CRFBean)
NewCRFBean(org.akaza.openclinica.bean.admin.NewCRFBean)
HSSFCell(org.apache.poi.hssf.usermodel.HSSFCell)
ScoreValidator(org.akaza.openclinica.logic.score.ScoreValidator)
HSSFSheet(org.apache.poi.hssf.usermodel.HSSFSheet)
CRFVersionBean(org.akaza.openclinica.bean.submit.CRFVersionBean)
ResponseSetBean(org.akaza.openclinica.bean.submit.ResponseSetBean)
ItemGroupBean(org.akaza.openclinica.bean.submit.ItemGroupBean)
ItemFormMetadataBean(org.akaza.openclinica.bean.submit.ItemFormMetadataBean)
Aggregations
NewCRFBean (org.akaza.openclinica.bean.admin.NewCRFBean)6
ArrayList (java.util.ArrayList)5
CRFVersionDAO (org.akaza.openclinica.dao.submit.CRFVersionDAO)5
IOException (java.io.IOException)4
ItemBean (org.akaza.openclinica.bean.submit.ItemBean)4
CRFDAO (org.akaza.openclinica.dao.admin.CRFDAO)4
CRFReadingException (org.akaza.openclinica.exception.CRFReadingException)4
CRFBean (org.akaza.openclinica.bean.admin.CRFBean)3
CRFVersionBean (org.akaza.openclinica.bean.submit.CRFVersionBean)3
EventCRFDAO (org.akaza.openclinica.dao.submit.EventCRFDAO)3
HSSFWorkbook (org.apache.poi.hssf.usermodel.HSSFWorkbook)3
File (java.io.File)2
Connection (java.sql.Connection)2
ResultSet (java.sql.ResultSet)2
SQLException (java.sql.SQLException)2
HashMap (java.util.HashMap)2
Pattern (java.util.regex.Pattern)2
PatternSyntaxException (java.util.regex.PatternSyntaxException)2
QueryObject (org.akaza.openclinica.bean.admin.QueryObject)2
SqlParameter (org.akaza.openclinica.bean.admin.SqlParameter)2
